Starting phenix.real_space_refine on Fri Sep 19 06:22:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.map" model { file = "/net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jc6_6534/09_2025/3jc6_6534.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 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 1 6.06 5 S 99 5.16 5 C 15099 2.51 5 N 4077 2.21 5 O 4456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23732 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1911 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 11, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "3" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2130 Classifications: {'peptide': 269} Link IDs: {'CIS': 12, 'PTRANS': 16, 'TRANS': 240} Chain breaks: 2 Chain: "4" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2203 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 19, 'PTRANS': 11, 'TRANS': 244} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2028 Classifications: {'peptide': 254} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 231} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2049 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 237} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "7" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Link IDs: {'CIS': 15, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 2 Chain: "E" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 Classifications: {'peptide': 553} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'CIS': 12, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 165} Chain breaks: 1 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11961 SG CYS 7 262 77.075 177.885 81.548 1.00167.77 S ATOM 12175 SG CYS 7 289 76.706 178.847 84.926 1.00194.98 S Time building chain proxies: 4.05, per 1000 atoms: 0.17 Number of scatterers: 23732 At special positions: 0 Unit cell: (169.68, 215.13, 111.1, 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 1 29.99 S 99 16.00 O 4456 8.00 N 4077 7.00 C 15099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 967.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 71001 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 289 " 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 27 sheets defined 39.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 3.894A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER 2 213 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 253 through 261 removed outlier: 3.919A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.998A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.523A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 removed outlier: 3.601A pdb=" N VAL 2 397 " --> pdb=" O PRO 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '3' and resid 19 through 32 removed outlier: 3.594A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 55 removed outlier: 3.646A pdb=" N ASN 3 49 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 102 through 107 removed outlier: 4.144A pdb=" N PHE 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 3.568A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 121 through 135 removed outlier: 3.551A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 removed outlier: 3.537A pdb=" N ALA 3 265 " --> pdb=" O PRO 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 Processing helix chain '4' and resid 189 through 196 Processing helix chain '4' and resid 226 through 237 removed outlier: 3.791A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.766A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.660A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 299 removed outlier: 3.571A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 Processing helix chain '5' and resid 22 through 37 removed outlier: 3.519A pdb=" N SER 5 30 " --> pdb=" O GLU 5 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 removed outlier: 4.053A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 72 through 80 removed outlier: 4.165A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 102 Proline residue: 5 88 - end of helix removed outlier: 3.622A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 279 through 283 Processing helix chain '6' and resid 106 through 121 removed outlier: 3.647A pdb=" N LYS 6 110 " --> pdb=" O VAL 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 144 Processing helix chain '6' and resid 155 through 161 removed outlier: 3.870A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 170 removed outlier: 4.039A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 6 170 " --> pdb=" O LEU 6 166 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 176 Processing helix chain '6' and resid 177 through 193 removed outlier: 3.820A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 25 removed outlier: 3.757A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.818A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 7 70 " --> pdb=" O MET 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.530A pdb=" N GLN 7 89 " --> pdb=" O ILE 7 85 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN 7 90 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 91 " --> pdb=" O GLN 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.771A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 115 Processing helix chain '7' and resid 119 through 125 removed outlier: 4.026A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 158 removed outlier: 3.599A pdb=" N LEU 7 143 " --> pdb=" O LEU 7 139 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 220 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain 'E' and resid 7 through 18 Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.780A pdb=" N LEU E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 4.203A pdb=" N ARG E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.521A pdb=" N PHE E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.929A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'E' and resid 152 through 157 removed outlier: 3.621A pdb=" N LYS E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 240 removed outlier: 3.945A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.611A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 301 removed outlier: 4.643A pdb=" N LEU E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 340 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.701A pdb=" N LYS E 347 " --> pdb=" O TYR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 367 removed outlier: 3.752A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS E 360 " --> pdb=" O LYS E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 removed outlier: 3.574A pdb=" N GLU E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.670A pdb=" N MET E 380 " --> pdb=" O TRP E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'E' and resid 397 through 400 Processing helix chain 'E' and resid 421 through 434 removed outlier: 3.662A pdb=" N VAL E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 483 removed outlier: 3.945A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 515 removed outlier: 3.572A pdb=" N LEU E 498 " --> pdb=" O ARG E 494 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 540 Processing helix chain 'E' and resid 541 through 557 removed outlier: 3.636A pdb=" N ALA E 557 " --> pdb=" O ILE E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 614 removed outlier: 3.589A pdb=" N ILE E 612 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 646 removed outlier: 4.484A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 105 removed outlier: 4.026A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 164 removed outlier: 3.641A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 198 Processing helix chain 'D' and resid 279 through 288 removed outlier: 5.006A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.867A pdb=" N GLN B 17 " --> pdb=" O PRO B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.782A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 4.029A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.220A pdb=" N PHE B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.653A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 199 removed outlier: 3.536A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.207A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 removed outlier: 4.021A pdb=" N ASN A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 4.008A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 104 removed outlier: 4.091A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.614A pdb=" N TYR A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 4.034A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.575A pdb=" N VAL C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.705A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 104 through 116 removed outlier: 4.395A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.970A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.743A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.549A pdb=" N PHE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain '2' and resid 331 through 333 removed outlier: 3.535A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain '2' and resid 331 through 333 removed outlier: 3.535A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain '3' and resid 179 through 180 removed outlier: 7.140A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain '3' and resid 210 through 213 Processing sheet with id=E, first strand: chain '4' and resid 332 through 335 removed outlier: 6.610A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain '4' and resid 339 through 342 Processing sheet with id=G, first strand: chain '4' and resid 344 through 345 Processing sheet with id=H, first strand: chain '4' and resid 365 through 366 removed outlier: 6.903A pdb=" N ILE 4 365 " --> pdb=" O THR 6 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=H Processing sheet with id=I, first strand: chain '4' and resid 435 through 436 Processing sheet with id=J, first strand: chain '4' and resid 439 through 442 Processing sheet with id=K, first strand: chain '5' and resid 60 through 63 removed outlier: 6.245A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=K Processing sheet with id=L, first strand: chain '5' and resid 298 through 301 removed outlier: 8.912A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL 5 292 " --> pdb=" O GLY 5 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain '5' and resid 190 through 193 removed outlier: 6.898A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain '6' and resid 150 through 154 removed outlier: 3.675A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain '6' and resid 273 through 274 Processing sheet with id=P, first strand: chain '6' and resid 454 through 456 removed outlier: 6.330A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain '6' and resid 404 through 405 Processing sheet with id=R, first strand: chain '7' and resid 77 through 81 Processing sheet with id=S, first strand: chain '7' and resid 252 through 253 removed outlier: 6.777A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain '7' and resid 252 through 253 removed outlier: 3.587A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain '7' and resid 269 through 270 removed outlier: 3.857A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'E' and resid 119 through 123 removed outlier: 6.944A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 28 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 58 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 188 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'E' and resid 318 through 321 removed outlier: 5.507A pdb=" N THR E 412 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE E 419 " --> pdb=" O THR E 412 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 414 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'E' and resid 569 through 571 removed outlier: 3.993A pdb=" N LEU E 569 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 582 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.020A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'B' and resid 69 through 72 Processing sheet with id=AA, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.607A pdb=" N LEU C 44 " --> pdb=" O CYS C 18 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2247 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: 3.24 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4109 1.32 - 1.45: 6553 1.45 - 1.58: 13334 1.58 - 1.71: 7 1.71 - 1.84: 156 Bond restraints: 24159 Sorted by residual: bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.540 1.620 -0.079 1.36e-02 5.41e+03 3.41e+01 bond pdb=" CA ILE 3 122 " pdb=" CB ILE 3 122 " ideal model delta sigma weight residual 1.537 1.560 -0.024 5.00e-03 4.00e+04 2.23e+01 bond pdb=" N MET C 191 " pdb=" CA MET C 191 " ideal model delta sigma weight residual 1.458 1.518 -0.060 1.27e-02 6.20e+03 2.20e+01 bond pdb=" CA VAL 3 139 " pdb=" CB VAL 3 139 " ideal model delta sigma weight residual 1.537 1.592 -0.055 1.29e-02 6.01e+03 1.82e+01 bond pdb=" N PRO 3 232 " pdb=" CD PRO 3 232 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 24154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 31872 4.11 - 8.21: 723 8.21 - 12.32: 66 12.32 - 16.43: 10 16.43 - 20.53: 3 Bond angle restraints: 32674 Sorted by residual: angle pdb=" C THR 5 325 " pdb=" N PRO 5 326 " pdb=" CA PRO 5 326 " ideal model delta sigma weight residual 119.83 140.36 -20.53 1.08e+00 8.57e-01 3.62e+02 angle pdb=" C GLU 4 378 " pdb=" N PRO 4 379 " pdb=" CA PRO 4 379 " ideal model delta sigma weight residual 119.56 134.51 -14.95 1.02e+00 9.61e-01 2.15e+02 angle pdb=" C CYS 6 333 " pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " ideal model delta sigma weight residual 119.84 136.20 -16.36 1.25e+00 6.40e-01 1.71e+02 angle pdb=" N LEU 7 94 " pdb=" CA LEU 7 94 " pdb=" C LEU 7 94 " ideal model delta sigma weight residual 111.36 123.86 -12.50 1.09e+00 8.42e-01 1.31e+02 angle pdb=" C MET 6 373 " pdb=" N PRO 6 374 " pdb=" CA PRO 6 374 " ideal model delta sigma weight residual 119.90 129.28 -9.38 1.02e+00 9.61e-01 8.46e+01 ... (remaining 32669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.96: 14292 26.96 - 53.93: 437 53.93 - 80.89: 40 80.89 - 107.86: 9 107.86 - 134.82: 1 Dihedral angle restraints: 14779 sinusoidal: 6075 harmonic: 8704 Sorted by residual: dihedral pdb=" CA ASN 4 377 " pdb=" C ASN 4 377 " pdb=" N GLU 4 378 " pdb=" CA GLU 4 378 " ideal model delta harmonic sigma weight residual -180.00 -45.18 -134.82 0 5.00e+00 4.00e-02 7.27e+02 dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 122.45 57.55 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA VAL 7 257 " pdb=" C VAL 7 257 " pdb=" N ILE 7 258 " pdb=" CA ILE 7 258 " ideal model delta harmonic sigma weight residual 0.00 43.85 -43.85 0 5.00e+00 4.00e-02 7.69e+01 ... (remaining 14776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3028 0.072 - 0.144: 616 0.144 - 0.216: 86 0.216 - 0.288: 8 0.288 - 0.361: 2 Chirality restraints: 3740 Sorted by residual: chirality pdb=" CA GLN A 206 " pdb=" N GLN A 206 " pdb=" C GLN A 206 " pdb=" CB GLN A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE 7 258 " pdb=" CA ILE 7 258 " pdb=" CG1 ILE 7 258 " pdb=" CG2 ILE 7 258 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG 4 373 " pdb=" N ARG 4 373 " pdb=" C ARG 4 373 " pdb=" CB ARG 4 373 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3737 not shown) Planarity restraints: 4183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 2 331 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO 2 332 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO 2 332 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO 2 332 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 122 " -0.046 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO 3 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO 3 123 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO 3 123 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 3 193 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO 3 194 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO 3 194 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 3 194 " 0.037 5.00e-02 4.00e+02 ... (remaining 4180 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 62 2.22 - 2.89: 9251 2.89 - 3.56: 34630 3.56 - 4.23: 53575 4.23 - 4.90: 87540 Nonbonded interactions: 185058 Sorted by model distance: nonbonded pdb=" O LYS C 83 " pdb=" OD1 ASN C 86 " model vdw 1.554 3.040 nonbonded pdb=" CG1 VAL A 165 " pdb=" CD2 LEU A 205 " model vdw 1.619 3.880 nonbonded pdb=" OE2 GLU B 187 " pdb=" CG2 ILE C 176 " model vdw 1.653 3.460 nonbonded pdb=" OE1 GLU 3 234 " pdb=" O GLY 3 238 " model vdw 1.666 3.040 nonbonded pdb=" CD1 LEU E 34 " pdb=" CD1 LEU E 543 " model vdw 1.727 3.880 ... (remaining 185053 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.710 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.009 0.418 24165 Z= 0.631 Angle : 1.564 34.993 32676 Z= 0.997 Chirality : 0.058 0.361 3740 Planarity : 0.006 0.072 4183 Dihedral : 12.912 134.823 9106 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 39.71 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.82 % Favored : 89.04 % Rotamer: Outliers : 0.87 % Allowed : 6.63 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.37 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.13), residues: 2883 helix: -3.14 (0.11), residues: 982 sheet: -2.24 (0.21), residues: 377 loop : -2.22 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 131 TYR 0.024 0.002 TYR E 325 PHE 0.026 0.003 PHE 6 454 TRP 0.019 0.003 TRP C 111 HIS 0.010 0.002 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00885 (24159) covalent geometry : angle 1.53979 (32674) SS BOND : bond 0.00928 ( 1) SS BOND : angle 34.90857 ( 2) hydrogen bonds : bond 0.19887 ( 799) hydrogen bonds : angle 10.15954 ( 2247) metal coordination : bond 0.10366 ( 2) Misc. bond : bond 0.28358 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1144 time to evaluate : 0.847 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: 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: 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: 2 232 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8195 (ttm-80) REVERT: 2 246 TYR cc_start: 0.7766 (t80) cc_final: 0.7546 (t80) REVERT: 2 263 CYS cc_start: 0.8077 (m) cc_final: 0.7396 (p) REVERT: 2 265 GLU cc_start: 0.8928 (tp30) cc_final: 0.8423 (tt0) REVERT: 2 277 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7771 (mt-10) REVERT: 2 283 TYR cc_start: 0.6191 (m-10) cc_final: 0.5644 (m-10) REVERT: 2 292 GLU cc_start: 0.8562 (tp30) cc_final: 0.7745 (tm-30) REVERT: 2 308 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8910 (mp0) REVERT: 2 319 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7409 (mtm180) REVERT: 2 352 PHE cc_start: 0.7932 (t80) cc_final: 0.7491 (t80) REVERT: 2 402 LEU cc_start: 0.7982 (mp) cc_final: 0.7521 (tt) REVERT: 2 423 GLU cc_start: 0.8410 (mp0) cc_final: 0.8187 (mp0) REVERT: 2 447 PHE cc_start: 0.8471 (m-10) cc_final: 0.8239 (m-10) REVERT: 3 23 ASP cc_start: 0.8869 (m-30) cc_final: 0.8649 (t0) REVERT: 3 105 GLU cc_start: 0.8936 (mp0) cc_final: 0.8566 (mp0) REVERT: 3 171 LEU cc_start: 0.7959 (tt) cc_final: 0.7738 (tp) REVERT: 3 178 LYS cc_start: 0.8626 (mttm) cc_final: 0.8139 (mtpt) REVERT: 3 193 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8239 (ttm-80) REVERT: 3 212 ARG cc_start: 0.7995 (tpp80) cc_final: 0.7400 (ttp80) REVERT: 3 261 MET cc_start: 0.8114 (mmm) cc_final: 0.7480 (mmm) REVERT: 3 272 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7966 (ttt90) REVERT: 3 275 ASP cc_start: 0.8331 (p0) cc_final: 0.8115 (p0) REVERT: 3 287 LYS cc_start: 0.8490 (pttm) cc_final: 0.8222 (ptmm) REVERT: 4 185 VAL cc_start: 0.8264 (t) cc_final: 0.7947 (m) REVERT: 4 190 CYS cc_start: 0.7838 (m) cc_final: 0.7635 (p) REVERT: 4 229 GLN cc_start: 0.8276 (mt0) cc_final: 0.7865 (mt0) REVERT: 4 232 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8591 (tm-30) REVERT: 4 267 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8575 (mp0) REVERT: 4 303 VAL cc_start: 0.8946 (t) cc_final: 0.8643 (m) REVERT: 4 326 ILE cc_start: 0.8811 (mt) cc_final: 0.8544 (pt) REVERT: 4 372 GLU cc_start: 0.7375 (mp0) cc_final: 0.7062 (mt-10) REVERT: 4 382 MET cc_start: 0.7498 (tpp) cc_final: 0.7272 (tpt) REVERT: 5 33 ASN cc_start: 0.8479 (m-40) cc_final: 0.8096 (t0) REVERT: 5 37 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8324 (mp0) REVERT: 5 46 TYR cc_start: 0.7457 (m-10) cc_final: 0.7178 (m-10) REVERT: 5 57 LYS cc_start: 0.8786 (mttt) cc_final: 0.8527 (mtmm) REVERT: 5 77 LYS cc_start: 0.8596 (tptt) cc_final: 0.8318 (tppt) REVERT: 5 78 LYS cc_start: 0.8798 (ptpt) cc_final: 0.8189 (ptpp) REVERT: 5 96 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7719 (tm-30) REVERT: 5 165 ILE cc_start: 0.8663 (mt) cc_final: 0.8358 (pt) REVERT: 5 175 ARG cc_start: 0.8977 (mtp180) cc_final: 0.8195 (mtp85) REVERT: 5 181 ILE cc_start: 0.8818 (mt) cc_final: 0.8569 (mm) REVERT: 5 257 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8555 (ttpt) REVERT: 5 275 THR cc_start: 0.8743 (m) cc_final: 0.8418 (p) REVERT: 5 287 ILE cc_start: 0.8783 (mp) cc_final: 0.8510 (tp) REVERT: 6 139 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9174 (tp-100) REVERT: 6 147 ASP cc_start: 0.5227 (m-30) cc_final: 0.3722 (t0) REVERT: 6 153 ILE cc_start: 0.7946 (pp) cc_final: 0.7420 (pp) REVERT: 6 168 MET cc_start: 0.8782 (mmt) cc_final: 0.8456 (mmp) REVERT: 6 174 TYR cc_start: 0.8436 (t80) cc_final: 0.7952 (t80) REVERT: 6 176 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8182 (ttt-90) REVERT: 6 191 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8167 (ttmm) REVERT: 6 269 ASN cc_start: 0.8846 (t0) cc_final: 0.8276 (t0) REVERT: 6 276 ILE cc_start: 0.8500 (pp) cc_final: 0.8193 (pt) REVERT: 6 283 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8754 (mmmm) REVERT: 6 303 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7600 (mt-10) REVERT: 6 355 ASP cc_start: 0.7964 (m-30) cc_final: 0.7547 (m-30) REVERT: 6 382 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7924 (ttt180) REVERT: 6 420 THR cc_start: 0.7364 (p) cc_final: 0.6941 (p) REVERT: 6 457 CYS cc_start: 0.9105 (p) cc_final: 0.8861 (p) REVERT: 7 15 ASN cc_start: 0.9082 (t0) cc_final: 0.8756 (t0) REVERT: 7 20 GLU cc_start: 0.9274 (tt0) cc_final: 0.8937 (tp30) REVERT: 7 73 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7923 (ttp80) REVERT: 7 88 TYR cc_start: 0.8402 (t80) cc_final: 0.8008 (t80) REVERT: 7 122 ASP cc_start: 0.9038 (t0) cc_final: 0.8721 (m-30) REVERT: 7 194 PRO cc_start: 0.7249 (Cg_endo) cc_final: 0.6776 (Cg_exo) REVERT: 7 203 TYR cc_start: 0.8613 (m-10) cc_final: 0.8380 (m-10) REVERT: 7 245 ILE cc_start: 0.7541 (mm) cc_final: 0.7081 (mm) REVERT: 7 252 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8303 (mmtt) REVERT: 7 256 GLU cc_start: 0.8795 (tp30) cc_final: 0.8371 (mp0) REVERT: 7 294 THR cc_start: 0.8114 (m) cc_final: 0.7719 (p) REVERT: 7 313 CYS cc_start: 0.8753 (p) cc_final: 0.8405 (m) REVERT: 7 321 GLN cc_start: 0.8577 (mt0) cc_final: 0.8046 (mp10) REVERT: 7 370 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7259 (mp) REVERT: 7 373 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8310 (mt-10) REVERT: E 72 SER cc_start: 0.8872 (t) cc_final: 0.8555 (p) REVERT: E 151 THR cc_start: 0.8176 (p) cc_final: 0.7961 (p) REVERT: E 241 TYR cc_start: 0.8077 (t80) cc_final: 0.7657 (t80) REVERT: E 264 GLU cc_start: 0.8305 (mp0) cc_final: 0.8054 (mp0) REVERT: E 294 LEU cc_start: 0.9342 (mt) cc_final: 0.9023 (mm) REVERT: E 311 LYS cc_start: 0.7563 (mmmt) cc_final: 0.6458 (mmtm) REVERT: E 325 TYR cc_start: 0.7635 (m-80) cc_final: 0.7423 (m-80) REVERT: E 339 TYR cc_start: 0.9094 (t80) cc_final: 0.8833 (t80) REVERT: E 349 SER cc_start: 0.9084 (m) cc_final: 0.8484 (t) REVERT: E 387 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 407 ASP cc_start: 0.8657 (m-30) cc_final: 0.8004 (m-30) REVERT: E 413 LEU cc_start: 0.6326 (tp) cc_final: 0.6077 (tp) REVERT: E 420 SER cc_start: 0.9109 (m) cc_final: 0.8648 (p) REVERT: E 429 THR cc_start: 0.8547 (p) cc_final: 0.8343 (m) REVERT: E 485 ASP cc_start: 0.8776 (m-30) cc_final: 0.8069 (p0) REVERT: E 487 ARG cc_start: 0.8821 (ptp-170) cc_final: 0.8508 (ptp90) REVERT: E 498 LEU cc_start: 0.8838 (mt) cc_final: 0.8589 (tt) REVERT: E 519 ILE cc_start: 0.7767 (mp) cc_final: 0.7373 (tp) REVERT: E 541 ASN cc_start: 0.8918 (t0) cc_final: 0.8610 (t0) REVERT: E 628 SER cc_start: 0.9007 (p) cc_final: 0.8582 (t) REVERT: D 58 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9103 (mt0) REVERT: D 64 MET cc_start: 0.9357 (mmm) cc_final: 0.9121 (mtm) REVERT: D 76 LEU cc_start: 0.9184 (tp) cc_final: 0.8800 (tp) REVERT: D 84 MET cc_start: 0.8017 (ttm) cc_final: 0.7735 (tmm) REVERT: D 85 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8789 (tptp) REVERT: D 93 MET cc_start: 0.8626 (mmp) cc_final: 0.8412 (tmm) REVERT: D 127 LEU cc_start: 0.8925 (tt) cc_final: 0.8671 (tp) REVERT: D 160 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8815 (tm-30) REVERT: D 218 MET cc_start: 0.8718 (mtp) cc_final: 0.8480 (mtp) REVERT: D 222 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7560 (Cg_exo) REVERT: D 230 ILE cc_start: 0.9395 (pt) cc_final: 0.8934 (pt) REVERT: D 290 LYS cc_start: 0.8933 (mttp) cc_final: 0.8476 (mmmt) REVERT: B 81 GLN cc_start: 0.9014 (tt0) cc_final: 0.8445 (pp30) REVERT: B 87 ILE cc_start: 0.8305 (tp) cc_final: 0.7980 (mt) REVERT: B 91 GLN cc_start: 0.8260 (pm20) cc_final: 0.7898 (tm-30) REVERT: B 174 SER cc_start: 0.8799 (t) cc_final: 0.8338 (p) REVERT: A 1 MET cc_start: 0.7589 (ptp) cc_final: 0.7100 (ptp) REVERT: A 2 TYR cc_start: 0.6825 (t80) cc_final: 0.5872 (t80) REVERT: A 4 ASP cc_start: 0.8883 (p0) cc_final: 0.8649 (p0) REVERT: A 27 VAL cc_start: 0.8394 (p) cc_final: 0.7925 (p) REVERT: A 32 TYR cc_start: 0.8661 (t80) cc_final: 0.8382 (t80) REVERT: A 35 ASP cc_start: 0.8973 (p0) cc_final: 0.8670 (p0) REVERT: A 49 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8749 (ttpp) REVERT: A 70 CYS cc_start: 0.9069 (m) cc_final: 0.8856 (t) REVERT: A 73 PHE cc_start: 0.8791 (t80) cc_final: 0.8424 (t80) REVERT: A 91 ARG cc_start: 0.8489 (ttt90) cc_final: 0.8160 (tpp80) REVERT: A 115 PHE cc_start: 0.6593 (m-80) cc_final: 0.6308 (m-80) REVERT: A 128 GLN cc_start: 0.9038 (tt0) cc_final: 0.8614 (mt0) REVERT: A 129 GLU cc_start: 0.9435 (tt0) cc_final: 0.8975 (mt-10) REVERT: A 137 LEU cc_start: 0.8952 (tt) cc_final: 0.8722 (tt) REVERT: A 151 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 183 LEU cc_start: 0.8407 (mm) cc_final: 0.7185 (mm) REVERT: A 197 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8126 (mt-10) REVERT: C 19 LYS cc_start: 0.9060 (pttp) cc_final: 0.8638 (pptt) REVERT: C 48 LEU cc_start: 0.9489 (tp) cc_final: 0.9229 (tt) REVERT: C 126 GLU cc_start: 0.9158 (tp30) cc_final: 0.8906 (mm-30) REVERT: C 176 ILE cc_start: 0.8807 (pp) cc_final: 0.8402 (mt) REVERT: C 179 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8914 (mtmt) REVERT: C 188 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8298 (tppt) outliers start: 23 outliers final: 10 residues processed: 1163 average time/residue: 0.2095 time to fit residues: 348.5603 Evaluate side-chains 698 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 686 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 177 ASN 4 184 ASN 4 287 ASN 5 49 GLN 5 53 ASN 5 58 ASN 5 145 GLN ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN ** 5 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 157 HIS 6 364 ASN 7 87 GLN 7 89 GLN E 26 GLN E 243 GLN E 286 GLN E 382 HIS ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 146 GLN B 179 ASN B 196 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.143338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116390 restraints weight = 50336.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.118149 restraints weight = 29418.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118519 restraints weight = 23562.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.119613 restraints weight = 20184.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119581 restraints weight = 18219.943| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24165 Z= 0.207 Angle : 1.032 13.605 32676 Z= 0.530 Chirality : 0.053 0.317 3740 Planarity : 0.006 0.073 4183 Dihedral : 6.946 73.648 3234 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.46 % Favored : 90.50 % Rotamer: Outliers : 3.96 % Allowed : 17.04 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.69 % Twisted Proline : 0.80 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.14), residues: 2883 helix: -1.33 (0.14), residues: 1024 sheet: -2.04 (0.23), residues: 368 loop : -1.83 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 141 TYR 0.025 0.002 TYR E 579 PHE 0.025 0.002 PHE 7 355 TRP 0.024 0.003 TRP D 224 HIS 0.009 0.001 HIS 4 386 Details of bonding type rmsd covalent geometry : bond 0.00430 (24159) covalent geometry : angle 1.03217 (32674) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.54758 ( 2) hydrogen bonds : bond 0.04895 ( 799) hydrogen bonds : angle 6.36123 ( 2247) metal coordination : bond 0.00421 ( 2) Misc. bond : bond 0.01215 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 800 time to evaluate : 1.018 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: 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: 2 240 GLU cc_start: 0.7072 (tt0) cc_final: 0.6815 (tt0) REVERT: 2 300 PHE cc_start: 0.7107 (t80) cc_final: 0.6844 (t80) REVERT: 2 384 ASN cc_start: 0.8195 (p0) cc_final: 0.7897 (p0) REVERT: 2 442 ASN cc_start: 0.6719 (p0) cc_final: 0.6213 (p0) REVERT: 3 138 ASP cc_start: 0.5137 (m-30) cc_final: 0.4865 (m-30) REVERT: 3 213 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: 3 234 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6675 (mm-30) REVERT: 3 250 PHE cc_start: 0.8259 (m-80) cc_final: 0.7974 (m-80) REVERT: 4 197 PHE cc_start: 0.6971 (t80) cc_final: 0.6698 (t80) REVERT: 4 393 ASP cc_start: 0.7179 (m-30) cc_final: 0.6967 (m-30) REVERT: 5 33 ASN cc_start: 0.7831 (m-40) cc_final: 0.7098 (t0) REVERT: 5 91 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7583 (mt-10) REVERT: 5 96 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7361 (tm-30) REVERT: 5 152 ASP cc_start: 0.7081 (t0) cc_final: 0.6762 (p0) REVERT: 6 136 TYR cc_start: 0.7369 (m-80) cc_final: 0.7078 (m-80) REVERT: 6 147 ASP cc_start: 0.4432 (m-30) cc_final: 0.3168 (t0) REVERT: 6 153 ILE cc_start: 0.7942 (pp) cc_final: 0.7705 (pt) REVERT: 6 155 TYR cc_start: 0.7436 (t80) cc_final: 0.7213 (t80) REVERT: 6 303 GLU cc_start: 0.5904 (mt-10) cc_final: 0.4345 (mt-10) REVERT: 6 356 TRP cc_start: 0.7403 (p-90) cc_final: 0.6819 (p-90) REVERT: 6 360 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7870 (ttm-80) REVERT: 6 364 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7262 (p0) REVERT: 7 192 PHE cc_start: 0.6261 (m-10) cc_final: 0.6022 (m-10) REVERT: 7 203 TYR cc_start: 0.8159 (m-80) cc_final: 0.7769 (m-10) REVERT: 7 231 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7851 (mmmt) REVERT: 7 270 PHE cc_start: 0.6866 (m-80) cc_final: 0.6301 (m-80) REVERT: E 339 TYR cc_start: 0.8576 (t80) cc_final: 0.8317 (t80) REVERT: E 349 SER cc_start: 0.8722 (m) cc_final: 0.8352 (t) REVERT: E 471 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8385 (mmtm) REVERT: E 482 ASP cc_start: 0.8190 (m-30) cc_final: 0.7856 (m-30) REVERT: E 628 SER cc_start: 0.8945 (p) cc_final: 0.8685 (t) REVERT: D 85 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8510 (tptp) REVERT: D 143 TYR cc_start: 0.8232 (t80) cc_final: 0.7924 (t80) REVERT: D 179 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: D 226 LYS cc_start: 0.8873 (tppt) cc_final: 0.8576 (tppt) REVERT: B 60 LEU cc_start: 0.5627 (tp) cc_final: 0.5420 (tp) REVERT: B 80 LYS cc_start: 0.9019 (tptp) cc_final: 0.8675 (tppp) REVERT: B 105 GLU cc_start: 0.7983 (tp30) cc_final: 0.7206 (tp30) REVERT: A 35 ASP cc_start: 0.8499 (p0) cc_final: 0.7810 (p0) REVERT: A 46 ASN cc_start: 0.8645 (t0) cc_final: 0.8151 (t0) REVERT: A 105 ASN cc_start: 0.5467 (m-40) cc_final: 0.5165 (t0) REVERT: A 128 GLN cc_start: 0.8576 (tt0) cc_final: 0.8297 (tm-30) REVERT: A 180 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7481 (t) outliers start: 105 outliers final: 47 residues processed: 858 average time/residue: 0.1755 time to fit residues: 227.2995 Evaluate side-chains 662 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 611 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 213 ASP Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 364 ASN Chi-restraints excluded: chain 6 residue 368 ILE Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 9 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 87 optimal weight: 0.0040 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 333 GLN ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 454 ASN 3 29 GLN 3 210 HIS 4 386 HIS 5 49 GLN 5 53 ASN 5 58 ASN 5 253 GLN 6 182 GLN 7 334 HIS E 22 HIS ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN A 90 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.139648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112428 restraints weight = 50858.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.112368 restraints weight = 27554.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113541 restraints weight = 22936.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114198 restraints weight = 19214.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114476 restraints weight = 17438.562| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24165 Z= 0.185 Angle : 0.949 13.589 32676 Z= 0.487 Chirality : 0.050 0.283 3740 Planarity : 0.006 0.099 4183 Dihedral : 6.356 57.457 3217 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.16 % Favored : 90.05 % Rotamer: Outliers : 4.30 % Allowed : 20.96 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.69 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.15), residues: 2883 helix: -0.69 (0.15), residues: 1033 sheet: -1.82 (0.24), residues: 385 loop : -1.85 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 394 TYR 0.028 0.002 TYR A 2 PHE 0.021 0.002 PHE 4 347 TRP 0.015 0.002 TRP C 111 HIS 0.012 0.001 HIS 4 354 Details of bonding type rmsd covalent geometry : bond 0.00392 (24159) covalent geometry : angle 0.94900 (32674) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.82807 ( 2) hydrogen bonds : bond 0.04098 ( 799) hydrogen bonds : angle 5.78629 ( 2247) metal coordination : bond 0.00049 ( 2) Misc. bond : bond 0.00298 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 656 time to evaluate : 0.976 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 382 TYR cc_start: 0.8668 (m-80) cc_final: 0.8216 (m-80) REVERT: 2 444 PHE cc_start: 0.8492 (m-80) cc_final: 0.8136 (m-80) REVERT: 3 193 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: 3 212 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8433 (ttp80) REVERT: 3 213 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: 3 290 ASP cc_start: 0.7953 (p0) cc_final: 0.7639 (t0) REVERT: 4 233 MET cc_start: 0.8100 (tpp) cc_final: 0.7828 (mmm) REVERT: 4 263 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8877 (t0) REVERT: 4 267 GLU cc_start: 0.8432 (mp0) cc_final: 0.8066 (mp0) REVERT: 4 302 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8293 (mptt) REVERT: 4 371 CYS cc_start: 0.6849 (OUTLIER) cc_final: 0.5564 (t) REVERT: 4 387 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8078 (t0) REVERT: 4 398 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8295 (pttm) REVERT: 4 458 LYS cc_start: 0.8784 (tptm) cc_final: 0.8512 (tptp) REVERT: 5 33 ASN cc_start: 0.7947 (m-40) cc_final: 0.7530 (m-40) REVERT: 5 37 GLU cc_start: 0.7930 (mp0) cc_final: 0.7448 (mp0) REVERT: 5 91 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7781 (mt-10) REVERT: 5 96 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7437 (tm-30) REVERT: 5 178 TYR cc_start: 0.8111 (t80) cc_final: 0.7910 (t80) REVERT: 5 179 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6798 (pp) REVERT: 5 255 PHE cc_start: 0.8111 (m-80) cc_final: 0.7884 (m-80) REVERT: 6 136 TYR cc_start: 0.7402 (m-80) cc_final: 0.7005 (m-80) REVERT: 6 143 MET cc_start: 0.7949 (tpt) cc_final: 0.7550 (tpt) REVERT: 6 147 ASP cc_start: 0.4722 (m-30) cc_final: 0.3329 (t0) REVERT: 6 155 TYR cc_start: 0.7781 (t80) cc_final: 0.7478 (t80) REVERT: 6 283 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8977 (mppt) REVERT: 7 153 MET cc_start: 0.4350 (mmp) cc_final: 0.3748 (mmt) REVERT: 7 203 TYR cc_start: 0.8172 (m-80) cc_final: 0.7692 (m-10) REVERT: 7 231 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7919 (mmmt) REVERT: 7 244 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7679 (tp) REVERT: 7 252 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7926 (mmmt) REVERT: 7 270 PHE cc_start: 0.7314 (m-80) cc_final: 0.6755 (m-80) REVERT: E 325 TYR cc_start: 0.7485 (m-80) cc_final: 0.7277 (m-80) REVERT: E 339 TYR cc_start: 0.8584 (t80) cc_final: 0.8201 (t80) REVERT: E 349 SER cc_start: 0.8821 (m) cc_final: 0.8359 (t) REVERT: E 407 ASP cc_start: 0.8005 (m-30) cc_final: 0.7706 (m-30) REVERT: E 471 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8343 (mmtm) REVERT: E 476 ASN cc_start: 0.8178 (t0) cc_final: 0.7874 (t0) REVERT: E 497 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: E 628 SER cc_start: 0.8984 (p) cc_final: 0.8542 (t) REVERT: D 85 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8473 (tptp) REVERT: D 92 SER cc_start: 0.9240 (t) cc_final: 0.8991 (p) REVERT: D 93 MET cc_start: 0.7376 (tmm) cc_final: 0.7064 (tmm) REVERT: D 202 MET cc_start: 0.6939 (tpp) cc_final: 0.6648 (tpp) REVERT: B 87 ILE cc_start: 0.8422 (mt) cc_final: 0.8097 (mt) REVERT: B 132 ASP cc_start: 0.7495 (p0) cc_final: 0.7281 (p0) REVERT: A 38 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8458 (ttm-80) REVERT: A 42 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: A 43 GLU cc_start: 0.8794 (tp30) cc_final: 0.8554 (tp30) REVERT: A 114 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6185 (p) REVERT: A 129 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8223 (mp0) REVERT: A 204 TYR cc_start: 0.7705 (m-80) cc_final: 0.7481 (m-80) REVERT: C 73 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6156 (tm-30) outliers start: 114 outliers final: 55 residues processed: 726 average time/residue: 0.1719 time to fit residues: 190.9895 Evaluate side-chains 638 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 573 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 290 HIS Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 212 ARG Chi-restraints excluded: chain 3 residue 213 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 263 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 334 ARG Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 387 ASN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 275 THR Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 368 ILE Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain C residue 79 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 224 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 44 optimal weight: 0.0170 chunk 125 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 0.0020 chunk 60 optimal weight: 7.9990 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN 3 239 ASN 4 386 HIS 5 259 GLN 6 173 GLN 6 364 ASN E 243 GLN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.141441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.113179 restraints weight = 51227.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.115567 restraints weight = 28133.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.116349 restraints weight = 21359.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116707 restraints weight = 17757.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.116903 restraints weight = 16719.140| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 24165 Z= 0.173 Angle : 0.938 15.924 32676 Z= 0.475 Chirality : 0.049 0.315 3740 Planarity : 0.005 0.110 4183 Dihedral : 5.991 48.623 3217 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.30 % Favored : 89.91 % Rotamer: Outliers : 4.64 % Allowed : 22.99 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.76 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.15), residues: 2883 helix: -0.34 (0.15), residues: 1034 sheet: -1.76 (0.25), residues: 368 loop : -1.90 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 141 TYR 0.033 0.002 TYR 4 264 PHE 0.029 0.002 PHE 5 90 TRP 0.015 0.001 TRP C 111 HIS 0.011 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00358 (24159) covalent geometry : angle 0.93798 (32674) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.54780 ( 2) hydrogen bonds : bond 0.03807 ( 799) hydrogen bonds : angle 5.42399 ( 2247) metal coordination : bond 0.00008 ( 2) Misc. bond : bond 0.00358 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 657 time to evaluate : 1.000 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 392 GLU cc_start: 0.7272 (tp30) cc_final: 0.6854 (mm-30) REVERT: 2 444 PHE cc_start: 0.8636 (m-80) cc_final: 0.8238 (m-80) REVERT: 3 166 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7993 (pp) REVERT: 3 193 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7658 (ttm-80) REVERT: 3 212 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8486 (ttp80) REVERT: 3 213 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: 3 290 ASP cc_start: 0.7895 (p0) cc_final: 0.7379 (m-30) REVERT: 4 267 GLU cc_start: 0.8422 (mp0) cc_final: 0.8171 (mp0) REVERT: 4 371 CYS cc_start: 0.6049 (OUTLIER) cc_final: 0.4997 (t) REVERT: 4 453 LEU cc_start: 0.8714 (mt) cc_final: 0.8485 (mt) REVERT: 5 51 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6847 (ttt90) REVERT: 5 91 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7714 (mt-10) REVERT: 5 96 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7462 (tm-30) REVERT: 5 178 TYR cc_start: 0.8094 (t80) cc_final: 0.7852 (t80) REVERT: 5 179 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6642 (pp) REVERT: 6 136 TYR cc_start: 0.7270 (m-80) cc_final: 0.6837 (m-80) REVERT: 6 147 ASP cc_start: 0.4692 (m-30) cc_final: 0.3288 (t0) REVERT: 6 155 TYR cc_start: 0.7707 (t80) cc_final: 0.7453 (t80) REVERT: 6 180 PHE cc_start: 0.7516 (m-80) cc_final: 0.7006 (m-80) REVERT: 6 288 LEU cc_start: 0.8461 (mp) cc_final: 0.8256 (mp) REVERT: 7 153 MET cc_start: 0.4400 (mmp) cc_final: 0.3878 (mmt) REVERT: 7 203 TYR cc_start: 0.8101 (m-80) cc_final: 0.7674 (m-10) REVERT: 7 231 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7828 (mmmt) REVERT: 7 244 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7737 (tp) REVERT: 7 252 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7934 (mmmt) REVERT: 7 270 PHE cc_start: 0.6987 (m-80) cc_final: 0.6558 (m-80) REVERT: E 51 LYS cc_start: 0.8672 (tppt) cc_final: 0.8457 (tppt) REVERT: E 339 TYR cc_start: 0.8536 (t80) cc_final: 0.8196 (t80) REVERT: E 349 SER cc_start: 0.8830 (m) cc_final: 0.8391 (t) REVERT: E 471 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8321 (mmtm) REVERT: E 476 ASN cc_start: 0.8065 (t0) cc_final: 0.7758 (t0) REVERT: E 628 SER cc_start: 0.8936 (p) cc_final: 0.8479 (t) REVERT: D 94 GLN cc_start: 0.8222 (tp40) cc_final: 0.7914 (tp40) REVERT: D 132 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 202 MET cc_start: 0.6941 (tpp) cc_final: 0.6734 (tpp) REVERT: B 63 MET cc_start: 0.7291 (mpp) cc_final: 0.6490 (mtt) REVERT: B 132 ASP cc_start: 0.7383 (p0) cc_final: 0.7149 (p0) REVERT: A 114 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6753 (p) REVERT: A 182 ASN cc_start: 0.8820 (t0) cc_final: 0.8560 (t0) REVERT: C 110 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8356 (mttp) outliers start: 123 outliers final: 74 residues processed: 737 average time/residue: 0.1701 time to fit residues: 192.8093 Evaluate side-chains 654 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 571 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 212 ARG Chi-restraints excluded: chain 3 residue 213 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 156 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 364 ASN Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 350 ASP Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 110 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 0.0370 chunk 128 optimal weight: 0.0770 chunk 256 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 177 ASN 3 239 ASN 4 386 HIS 5 49 GLN 6 157 HIS 7 112 HIS E 231 HIS ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 ASN D 58 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN A 118 GLN A 128 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.112448 restraints weight = 51189.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.115258 restraints weight = 28525.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115476 restraints weight = 20322.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116226 restraints weight = 17740.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116284 restraints weight = 16437.160| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24165 Z= 0.172 Angle : 0.923 14.168 32676 Z= 0.467 Chirality : 0.049 0.276 3740 Planarity : 0.005 0.076 4183 Dihedral : 5.749 38.785 3213 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.47 % Favored : 89.73 % Rotamer: Outliers : 4.98 % Allowed : 24.43 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.76 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.15), residues: 2883 helix: -0.14 (0.16), residues: 1039 sheet: -1.61 (0.25), residues: 385 loop : -1.94 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 494 TYR 0.033 0.002 TYR 4 264 PHE 0.027 0.002 PHE 2 300 TRP 0.017 0.001 TRP C 111 HIS 0.010 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00365 (24159) covalent geometry : angle 0.92328 (32674) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.43617 ( 2) hydrogen bonds : bond 0.03654 ( 799) hydrogen bonds : angle 5.26124 ( 2247) metal coordination : bond 0.00036 ( 2) Misc. bond : bond 0.00400 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 603 time to evaluate : 0.967 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: 2 263 CYS cc_start: 0.7352 (m) cc_final: 0.7055 (p) REVERT: 2 392 GLU cc_start: 0.7373 (tp30) cc_final: 0.7154 (mm-30) REVERT: 2 434 TYR cc_start: 0.6911 (p90) cc_final: 0.6652 (p90) REVERT: 2 444 PHE cc_start: 0.8674 (m-80) cc_final: 0.8324 (m-80) REVERT: 3 166 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7951 (pp) REVERT: 3 212 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8438 (ttp80) REVERT: 3 213 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: 3 233 THR cc_start: 0.6050 (m) cc_final: 0.5672 (p) REVERT: 3 290 ASP cc_start: 0.7911 (p0) cc_final: 0.7348 (m-30) REVERT: 4 267 GLU cc_start: 0.8378 (mp0) cc_final: 0.8134 (mp0) REVERT: 4 278 ASP cc_start: 0.7167 (m-30) cc_final: 0.6779 (m-30) REVERT: 4 347 PHE cc_start: 0.8422 (m-80) cc_final: 0.7927 (m-80) REVERT: 4 371 CYS cc_start: 0.5763 (OUTLIER) cc_final: 0.5445 (t) REVERT: 4 458 LYS cc_start: 0.8668 (tptp) cc_final: 0.8460 (tptp) REVERT: 5 51 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6682 (ttt90) REVERT: 5 77 LYS cc_start: 0.8775 (tppt) cc_final: 0.8507 (tptm) REVERT: 5 91 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7730 (mt-10) REVERT: 5 96 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7477 (tm-30) REVERT: 5 178 TYR cc_start: 0.8101 (t80) cc_final: 0.7845 (t80) REVERT: 6 136 TYR cc_start: 0.7216 (m-80) cc_final: 0.6674 (m-80) REVERT: 6 143 MET cc_start: 0.7648 (tpt) cc_final: 0.7331 (tpt) REVERT: 6 147 ASP cc_start: 0.4607 (m-30) cc_final: 0.3341 (t0) REVERT: 6 172 GLU cc_start: 0.8307 (mp0) cc_final: 0.7806 (mp0) REVERT: 6 180 PHE cc_start: 0.7571 (m-80) cc_final: 0.7250 (m-80) REVERT: 6 288 LEU cc_start: 0.8569 (mp) cc_final: 0.8355 (mt) REVERT: 7 153 MET cc_start: 0.4441 (mmp) cc_final: 0.3898 (mmt) REVERT: 7 203 TYR cc_start: 0.8115 (m-80) cc_final: 0.7708 (m-10) REVERT: 7 228 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7616 (mpp80) REVERT: 7 231 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7937 (mmmt) REVERT: 7 244 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7701 (tp) REVERT: 7 252 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7805 (mmmm) REVERT: E 339 TYR cc_start: 0.8625 (t80) cc_final: 0.8263 (t80) REVERT: E 349 SER cc_start: 0.8863 (m) cc_final: 0.8427 (t) REVERT: E 476 ASN cc_start: 0.8037 (t0) cc_final: 0.7604 (t0) REVERT: E 605 PHE cc_start: 0.7932 (m-80) cc_final: 0.7478 (m-80) REVERT: E 628 SER cc_start: 0.8943 (p) cc_final: 0.8487 (t) REVERT: D 93 MET cc_start: 0.7389 (tmm) cc_final: 0.7188 (ppp) REVERT: D 257 THR cc_start: 0.6533 (p) cc_final: 0.6184 (p) REVERT: B 63 MET cc_start: 0.7260 (mpp) cc_final: 0.6489 (mtt) REVERT: B 104 TYR cc_start: 0.7993 (t80) cc_final: 0.7677 (t80) REVERT: B 105 GLU cc_start: 0.8152 (tp30) cc_final: 0.7889 (mm-30) REVERT: B 132 ASP cc_start: 0.7391 (p0) cc_final: 0.7152 (p0) REVERT: A 87 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 129 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7925 (mp0) REVERT: A 182 ASN cc_start: 0.8818 (t0) cc_final: 0.8569 (t0) REVERT: A 204 TYR cc_start: 0.7354 (m-80) cc_final: 0.7127 (m-80) outliers start: 132 outliers final: 84 residues processed: 689 average time/residue: 0.1593 time to fit residues: 170.0189 Evaluate side-chains 656 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 564 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 207 ILE Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 212 ARG Chi-restraints excluded: chain 3 residue 213 ASP Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 191 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 226 SER Chi-restraints excluded: chain 7 residue 228 ARG Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 386 HIS 5 259 GLN 6 139 GLN 7 16 ASN E 13 ASN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN D 94 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106451 restraints weight = 51008.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108053 restraints weight = 29277.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108597 restraints weight = 24190.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109336 restraints weight = 19692.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109467 restraints weight = 18044.314| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24165 Z= 0.218 Angle : 0.953 14.552 32676 Z= 0.483 Chirality : 0.051 0.262 3740 Planarity : 0.007 0.311 4183 Dihedral : 6.240 137.461 3213 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.85 % Favored : 89.39 % Rotamer: Outliers : 5.88 % Allowed : 24.16 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.87 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.15), residues: 2883 helix: -0.08 (0.16), residues: 1040 sheet: -1.71 (0.25), residues: 393 loop : -2.05 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG D 141 TYR 0.031 0.002 TYR 4 264 PHE 0.026 0.002 PHE A 115 TRP 0.037 0.002 TRP C 111 HIS 0.008 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00489 (24159) covalent geometry : angle 0.95292 (32674) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.36692 ( 2) hydrogen bonds : bond 0.03781 ( 799) hydrogen bonds : angle 5.20849 ( 2247) metal coordination : bond 0.00045 ( 2) Misc. bond : bond 0.00293 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 581 time to evaluate : 1.036 Fit side-chains revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 335 LYS cc_start: 0.6761 (mmtp) cc_final: 0.6355 (mttp) REVERT: 2 338 LYS cc_start: 0.7602 (ttpp) cc_final: 0.7397 (ttpp) REVERT: 2 383 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7438 (mtt180) REVERT: 2 444 PHE cc_start: 0.8740 (m-80) cc_final: 0.8398 (m-80) REVERT: 3 166 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7819 (pp) REVERT: 3 179 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8841 (tp) REVERT: 3 193 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: 3 214 TYR cc_start: 0.7242 (m-10) cc_final: 0.6929 (m-10) REVERT: 3 233 THR cc_start: 0.6469 (m) cc_final: 0.6126 (p) REVERT: 4 262 LEU cc_start: 0.8410 (tp) cc_final: 0.8166 (pp) REVERT: 4 278 ASP cc_start: 0.7214 (m-30) cc_final: 0.6795 (m-30) REVERT: 4 302 LYS cc_start: 0.8323 (ptpp) cc_final: 0.7621 (ptpp) REVERT: 4 371 CYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4846 (m) REVERT: 4 417 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6542 (pt) REVERT: 5 51 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6808 (ttt90) REVERT: 5 77 LYS cc_start: 0.8774 (tppt) cc_final: 0.8500 (tptm) REVERT: 5 91 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7859 (mt-10) REVERT: 5 96 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7664 (tm-30) REVERT: 6 136 TYR cc_start: 0.7365 (m-80) cc_final: 0.6828 (m-80) REVERT: 6 147 ASP cc_start: 0.4913 (m-30) cc_final: 0.3415 (t0) REVERT: 6 155 TYR cc_start: 0.7785 (t80) cc_final: 0.7481 (t80) REVERT: 6 172 GLU cc_start: 0.8431 (mp0) cc_final: 0.7801 (mp0) REVERT: 6 180 PHE cc_start: 0.7749 (m-80) cc_final: 0.7410 (m-80) REVERT: 6 288 LEU cc_start: 0.8697 (mp) cc_final: 0.8439 (mt) REVERT: 7 203 TYR cc_start: 0.8404 (m-80) cc_final: 0.7980 (m-10) REVERT: 7 231 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8351 (mmmt) REVERT: 7 244 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7833 (tp) REVERT: 7 252 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7887 (mmmm) REVERT: 7 320 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7266 (mp-120) REVERT: E 51 LYS cc_start: 0.8787 (tppt) cc_final: 0.8558 (tppt) REVERT: E 338 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: E 339 TYR cc_start: 0.8767 (t80) cc_final: 0.8383 (t80) REVERT: E 349 SER cc_start: 0.8988 (m) cc_final: 0.8511 (t) REVERT: E 497 GLN cc_start: 0.7356 (mt0) cc_final: 0.7121 (mt0) REVERT: E 498 LEU cc_start: 0.8868 (tt) cc_final: 0.8644 (tp) REVERT: E 605 PHE cc_start: 0.8072 (m-80) cc_final: 0.7601 (m-80) REVERT: E 611 GLN cc_start: 0.7155 (pp30) cc_final: 0.6869 (pp30) REVERT: E 628 SER cc_start: 0.9006 (p) cc_final: 0.8518 (t) REVERT: D 132 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7893 (tm-30) REVERT: D 202 MET cc_start: 0.6938 (tpp) cc_final: 0.6607 (tpp) REVERT: D 257 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6606 (p) REVERT: B 63 MET cc_start: 0.7289 (mpp) cc_final: 0.6593 (mtt) REVERT: B 105 GLU cc_start: 0.8323 (tp30) cc_final: 0.8026 (mm-30) REVERT: B 132 ASP cc_start: 0.7650 (p0) cc_final: 0.7407 (p0) REVERT: A 34 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 87 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9217 (mm) REVERT: A 110 MET cc_start: 0.0186 (OUTLIER) cc_final: -0.0645 (tpt) REVERT: A 182 ASN cc_start: 0.8849 (t0) cc_final: 0.8641 (t0) REVERT: A 204 TYR cc_start: 0.7671 (m-80) cc_final: 0.7442 (m-80) REVERT: C 116 SER cc_start: 0.8475 (t) cc_final: 0.8076 (p) outliers start: 157 outliers final: 100 residues processed: 696 average time/residue: 0.1674 time to fit residues: 182.1115 Evaluate side-chains 656 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 545 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 207 ILE Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 321 THR Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 179 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 191 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 93 PHE Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 339 LEU Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 218 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 18 optimal weight: 0.0030 chunk 108 optimal weight: 6.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 333 GLN ** 3 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 177 ASN 3 239 ASN 4 386 HIS ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN 5 259 GLN 6 362 GLN 7 107 GLN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 604 ASN D 109 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 59 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.133897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.104802 restraints weight = 50599.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106485 restraints weight = 28642.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106946 restraints weight = 23791.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107574 restraints weight = 19408.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107732 restraints weight = 17855.020| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24165 Z= 0.226 Angle : 0.958 14.002 32676 Z= 0.485 Chirality : 0.051 0.247 3740 Planarity : 0.005 0.077 4183 Dihedral : 6.550 171.739 3213 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.27 % Favored : 88.97 % Rotamer: Outliers : 6.26 % Allowed : 25.29 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.83 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.15), residues: 2883 helix: -0.02 (0.16), residues: 1049 sheet: -1.86 (0.25), residues: 403 loop : -2.11 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 38 TYR 0.034 0.002 TYR 4 264 PHE 0.032 0.002 PHE 4 300 TRP 0.037 0.002 TRP C 111 HIS 0.011 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00513 (24159) covalent geometry : angle 0.95832 (32674) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.33705 ( 2) hydrogen bonds : bond 0.03750 ( 799) hydrogen bonds : angle 5.17657 ( 2247) metal coordination : bond 0.00075 ( 2) Misc. bond : bond 0.00285 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 553 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 289 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (mm) REVERT: 2 434 TYR cc_start: 0.6883 (p90) cc_final: 0.6634 (p90) REVERT: 2 444 PHE cc_start: 0.8777 (m-80) cc_final: 0.8533 (m-80) REVERT: 3 179 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8821 (tp) REVERT: 3 193 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7908 (ttm-80) REVERT: 3 233 THR cc_start: 0.6725 (m) cc_final: 0.6377 (p) REVERT: 4 278 ASP cc_start: 0.7280 (m-30) cc_final: 0.6919 (m-30) REVERT: 4 371 CYS cc_start: 0.5610 (OUTLIER) cc_final: 0.5178 (t) REVERT: 4 386 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7848 (m-70) REVERT: 4 417 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6717 (pt) REVERT: 5 51 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6871 (ttt90) REVERT: 5 77 LYS cc_start: 0.8736 (tppt) cc_final: 0.8451 (tptm) REVERT: 5 90 PHE cc_start: 0.6831 (t80) cc_final: 0.6505 (t80) REVERT: 5 96 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7688 (tm-30) REVERT: 5 197 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: 5 331 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7642 (pp) REVERT: 6 136 TYR cc_start: 0.7388 (m-80) cc_final: 0.6840 (m-80) REVERT: 6 143 MET cc_start: 0.7801 (tpt) cc_final: 0.7382 (tpt) REVERT: 6 147 ASP cc_start: 0.4699 (m-30) cc_final: 0.3346 (t0) REVERT: 6 168 MET cc_start: 0.8917 (mmm) cc_final: 0.8469 (mmm) REVERT: 6 172 GLU cc_start: 0.8410 (mp0) cc_final: 0.7777 (mp0) REVERT: 6 180 PHE cc_start: 0.7766 (m-80) cc_final: 0.7371 (m-80) REVERT: 6 288 LEU cc_start: 0.8720 (mp) cc_final: 0.8498 (mt) REVERT: 6 305 TYR cc_start: 0.8214 (t80) cc_final: 0.8011 (t80) REVERT: 6 450 TYR cc_start: 0.8307 (m-10) cc_final: 0.7943 (m-10) REVERT: 7 203 TYR cc_start: 0.8329 (m-80) cc_final: 0.8113 (m-10) REVERT: 7 225 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8525 (pp) REVERT: 7 231 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8398 (mmmt) REVERT: 7 245 ILE cc_start: 0.7226 (mm) cc_final: 0.7003 (mm) REVERT: 7 252 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7857 (mmmm) REVERT: 7 320 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7314 (mp-120) REVERT: E 19 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7626 (m) REVERT: E 338 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: E 339 TYR cc_start: 0.8794 (t80) cc_final: 0.8415 (t80) REVERT: E 402 GLN cc_start: 0.7956 (tp40) cc_final: 0.7516 (tm-30) REVERT: E 605 PHE cc_start: 0.8173 (m-80) cc_final: 0.7712 (m-80) REVERT: E 628 SER cc_start: 0.8996 (p) cc_final: 0.8529 (t) REVERT: D 132 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7855 (tm-30) REVERT: D 202 MET cc_start: 0.7155 (tpp) cc_final: 0.6794 (tpp) REVERT: D 257 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6656 (p) REVERT: B 63 MET cc_start: 0.7304 (mpp) cc_final: 0.6549 (mtt) REVERT: B 132 ASP cc_start: 0.7663 (p0) cc_final: 0.7454 (p0) REVERT: A 34 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 87 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9239 (mm) REVERT: A 182 ASN cc_start: 0.8854 (t0) cc_final: 0.8647 (t0) REVERT: C 109 ILE cc_start: 0.8944 (mt) cc_final: 0.8736 (mt) REVERT: C 116 SER cc_start: 0.8603 (t) cc_final: 0.8236 (p) outliers start: 167 outliers final: 112 residues processed: 675 average time/residue: 0.1587 time to fit residues: 167.4916 Evaluate side-chains 654 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 528 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 289 ILE Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 321 THR Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 378 GLU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 179 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 239 ASN Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 263 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 386 HIS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 191 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 260 GLU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 331 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 7 residue 16 ASN Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 93 PHE Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 339 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain C residue 184 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 266 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 177 ASN 3 239 ASN 4 386 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN E 141 GLN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 611 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.133922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104826 restraints weight = 50580.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106725 restraints weight = 28388.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107183 restraints weight = 23100.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107610 restraints weight = 19200.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.107828 restraints weight = 17759.375| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24165 Z= 0.207 Angle : 0.966 14.122 32676 Z= 0.487 Chirality : 0.051 0.404 3740 Planarity : 0.005 0.089 4183 Dihedral : 6.450 169.139 3212 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.02 % Favored : 89.21 % Rotamer: Outliers : 5.35 % Allowed : 26.42 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.91 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.15), residues: 2883 helix: 0.07 (0.16), residues: 1049 sheet: -1.89 (0.25), residues: 393 loop : -2.14 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 38 TYR 0.025 0.002 TYR E 241 PHE 0.038 0.002 PHE 4 300 TRP 0.038 0.002 TRP C 111 HIS 0.011 0.001 HIS 3 175 Details of bonding type rmsd covalent geometry : bond 0.00467 (24159) covalent geometry : angle 0.96557 (32674) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.31203 ( 2) hydrogen bonds : bond 0.03738 ( 799) hydrogen bonds : angle 5.14622 ( 2247) metal coordination : bond 0.00027 ( 2) Misc. bond : bond 0.00748 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 550 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 289 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8080 (mm) REVERT: 2 434 TYR cc_start: 0.6880 (p90) cc_final: 0.6647 (p90) REVERT: 2 444 PHE cc_start: 0.8792 (m-80) cc_final: 0.8466 (m-80) REVERT: 3 179 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (tp) REVERT: 3 193 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: 3 233 THR cc_start: 0.6759 (m) cc_final: 0.6421 (p) REVERT: 4 263 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8657 (t0) REVERT: 4 371 CYS cc_start: 0.5353 (OUTLIER) cc_final: 0.4902 (t) REVERT: 4 386 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7985 (m-70) REVERT: 4 417 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6809 (pt) REVERT: 5 51 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6920 (ttt90) REVERT: 5 77 LYS cc_start: 0.8728 (tppt) cc_final: 0.8445 (tptm) REVERT: 5 96 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7701 (tm-30) REVERT: 5 197 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.5484 (m-80) REVERT: 6 136 TYR cc_start: 0.7390 (m-80) cc_final: 0.6824 (m-80) REVERT: 6 143 MET cc_start: 0.7861 (tpt) cc_final: 0.7444 (tpt) REVERT: 6 147 ASP cc_start: 0.4649 (m-30) cc_final: 0.3360 (t0) REVERT: 6 155 TYR cc_start: 0.7686 (t80) cc_final: 0.7454 (t80) REVERT: 6 168 MET cc_start: 0.8911 (mmm) cc_final: 0.8460 (mmm) REVERT: 6 172 GLU cc_start: 0.8410 (mp0) cc_final: 0.7767 (mp0) REVERT: 6 180 PHE cc_start: 0.7745 (m-80) cc_final: 0.7368 (m-80) REVERT: 6 288 LEU cc_start: 0.8712 (mp) cc_final: 0.8477 (mt) REVERT: 6 450 TYR cc_start: 0.8361 (m-10) cc_final: 0.8001 (m-10) REVERT: 7 203 TYR cc_start: 0.8345 (m-80) cc_final: 0.8098 (m-10) REVERT: 7 231 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8428 (mmmt) REVERT: 7 245 ILE cc_start: 0.7127 (mm) cc_final: 0.6905 (mm) REVERT: 7 252 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7844 (mmmm) REVERT: 7 292 ASN cc_start: 0.4966 (OUTLIER) cc_final: 0.4605 (p0) REVERT: 7 320 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7297 (mp-120) REVERT: 7 367 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5891 (mtmm) REVERT: E 8 PHE cc_start: 0.6633 (m-80) cc_final: 0.6432 (m-80) REVERT: E 19 SER cc_start: 0.8010 (OUTLIER) cc_final: 0.7618 (m) REVERT: E 338 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8491 (m-10) REVERT: E 339 TYR cc_start: 0.8770 (t80) cc_final: 0.8410 (t80) REVERT: E 402 GLN cc_start: 0.7920 (tp40) cc_final: 0.7507 (tm-30) REVERT: E 605 PHE cc_start: 0.8157 (m-80) cc_final: 0.7704 (m-80) REVERT: E 628 SER cc_start: 0.8998 (p) cc_final: 0.8505 (t) REVERT: D 64 MET cc_start: 0.8985 (mmm) cc_final: 0.8391 (tpp) REVERT: D 132 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 202 MET cc_start: 0.7130 (tpp) cc_final: 0.6786 (tpp) REVERT: D 216 VAL cc_start: 0.8576 (p) cc_final: 0.8255 (t) REVERT: D 257 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6657 (p) REVERT: D 260 ILE cc_start: 0.8675 (tt) cc_final: 0.8450 (pt) REVERT: B 63 MET cc_start: 0.7295 (mpp) cc_final: 0.6548 (mtt) REVERT: B 132 ASP cc_start: 0.7668 (p0) cc_final: 0.7427 (p0) REVERT: A 87 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9217 (mm) REVERT: A 182 ASN cc_start: 0.8849 (t0) cc_final: 0.8631 (t0) REVERT: C 186 ASP cc_start: 0.7703 (m-30) cc_final: 0.7501 (m-30) REVERT: C 191 MET cc_start: 0.8261 (mmm) cc_final: 0.8009 (mmt) REVERT: C 193 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7254 (mmmt) outliers start: 143 outliers final: 109 residues processed: 654 average time/residue: 0.1655 time to fit residues: 168.6607 Evaluate side-chains 653 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 529 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 289 ILE Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 321 THR Chi-restraints excluded: chain 2 residue 328 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 378 GLU Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 438 LEU Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 179 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 239 ASN Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 263 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 386 HIS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 191 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 260 GLU Chi-restraints excluded: chain 5 residue 299 SER Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 7 residue 16 ASN Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 93 PHE Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 292 ASN Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 367 LYS Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 184 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 232 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 215 optimal weight: 0.0170 chunk 49 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 177 ASN 3 239 ASN 4 386 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 611 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN A 175 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.136847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108932 restraints weight = 50396.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108453 restraints weight = 29889.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109711 restraints weight = 24074.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110151 restraints weight = 19367.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.110423 restraints weight = 18228.552| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24165 Z= 0.174 Angle : 0.972 16.740 32676 Z= 0.486 Chirality : 0.051 0.344 3740 Planarity : 0.005 0.077 4183 Dihedral : 6.350 170.616 3212 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.85 % Favored : 89.42 % Rotamer: Outliers : 4.45 % Allowed : 27.74 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.91 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.15), residues: 2883 helix: 0.19 (0.16), residues: 1037 sheet: -1.90 (0.26), residues: 375 loop : -2.08 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 6 187 TYR 0.025 0.002 TYR E 241 PHE 0.040 0.002 PHE 4 300 TRP 0.031 0.002 TRP C 111 HIS 0.010 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00371 (24159) covalent geometry : angle 0.97203 (32674) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.34586 ( 2) hydrogen bonds : bond 0.03632 ( 799) hydrogen bonds : angle 5.09310 ( 2247) metal coordination : bond 0.00041 ( 2) Misc. bond : bond 0.00657 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 580 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 289 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7837 (mm) REVERT: 2 434 TYR cc_start: 0.6940 (p90) cc_final: 0.6714 (p90) REVERT: 2 444 PHE cc_start: 0.8816 (m-80) cc_final: 0.8521 (m-80) REVERT: 3 179 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8889 (tp) REVERT: 3 193 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7793 (ttm-80) REVERT: 3 233 THR cc_start: 0.6423 (m) cc_final: 0.6106 (p) REVERT: 4 278 ASP cc_start: 0.7245 (m-30) cc_final: 0.6954 (m-30) REVERT: 4 325 LEU cc_start: 0.8613 (mm) cc_final: 0.8402 (mt) REVERT: 4 356 MET cc_start: 0.8458 (ppp) cc_final: 0.8236 (ppp) REVERT: 4 371 CYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5075 (t) REVERT: 4 417 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6425 (pt) REVERT: 5 51 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6831 (ttt90) REVERT: 5 77 LYS cc_start: 0.8690 (tppt) cc_final: 0.8411 (tptm) REVERT: 5 99 LYS cc_start: 0.8778 (tppt) cc_final: 0.8349 (mptt) REVERT: 6 143 MET cc_start: 0.7854 (tpt) cc_final: 0.7487 (tpt) REVERT: 6 147 ASP cc_start: 0.4668 (m-30) cc_final: 0.3515 (t0) REVERT: 6 168 MET cc_start: 0.8932 (mmm) cc_final: 0.8421 (mmm) REVERT: 6 172 GLU cc_start: 0.8389 (mp0) cc_final: 0.7747 (mp0) REVERT: 6 180 PHE cc_start: 0.7743 (m-80) cc_final: 0.7334 (m-80) REVERT: 6 288 LEU cc_start: 0.8655 (mp) cc_final: 0.8445 (mt) REVERT: 6 450 TYR cc_start: 0.8341 (m-10) cc_final: 0.8114 (m-10) REVERT: 7 122 ASP cc_start: 0.8717 (m-30) cc_final: 0.8262 (t0) REVERT: 7 153 MET cc_start: 0.3967 (mmp) cc_final: 0.3319 (mmt) REVERT: 7 231 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8184 (mmmt) REVERT: 7 245 ILE cc_start: 0.7122 (mm) cc_final: 0.6900 (mm) REVERT: 7 252 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7848 (mmmm) REVERT: 7 320 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: E 338 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8634 (m-10) REVERT: E 339 TYR cc_start: 0.8685 (t80) cc_final: 0.8347 (t80) REVERT: E 402 GLN cc_start: 0.7914 (tp40) cc_final: 0.7499 (tm-30) REVERT: E 605 PHE cc_start: 0.8209 (m-80) cc_final: 0.7746 (m-80) REVERT: E 628 SER cc_start: 0.8969 (p) cc_final: 0.8445 (t) REVERT: D 64 MET cc_start: 0.8933 (mmm) cc_final: 0.8304 (tpp) REVERT: D 132 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7896 (tm-30) REVERT: D 202 MET cc_start: 0.7110 (tpp) cc_final: 0.6798 (tpp) REVERT: D 226 LYS cc_start: 0.8890 (tppt) cc_final: 0.8440 (tppt) REVERT: D 257 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6435 (p) REVERT: D 260 ILE cc_start: 0.8592 (tt) cc_final: 0.8364 (pt) REVERT: B 63 MET cc_start: 0.7318 (mpp) cc_final: 0.6706 (mtt) REVERT: B 132 ASP cc_start: 0.7636 (p0) cc_final: 0.7399 (p0) REVERT: A 87 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9196 (mm) REVERT: A 182 ASN cc_start: 0.8847 (t0) cc_final: 0.8620 (t0) REVERT: C 113 MET cc_start: 0.7363 (mmt) cc_final: 0.7107 (mmp) REVERT: C 116 SER cc_start: 0.8559 (t) cc_final: 0.8189 (p) REVERT: C 186 ASP cc_start: 0.7667 (m-30) cc_final: 0.7441 (m-30) REVERT: C 191 MET cc_start: 0.8189 (mmm) cc_final: 0.7983 (mmt) REVERT: C 193 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7222 (mmmt) outliers start: 119 outliers final: 94 residues processed: 662 average time/residue: 0.1577 time to fit residues: 162.0513 Evaluate side-chains 643 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 540 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 289 ILE Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 378 GLU Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 179 LEU Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 239 ASN Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 263 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 344 VAL Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 386 HIS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 93 PHE Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain C residue 7 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 281 optimal weight: 0.0870 chunk 249 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 386 GLN 3 239 ASN 4 386 HIS 5 96 GLN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN E 531 GLN D 82 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108338 restraints weight = 50699.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110389 restraints weight = 29326.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111041 restraints weight = 21214.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111384 restraints weight = 18466.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.111596 restraints weight = 17283.226| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24165 Z= 0.177 Angle : 0.987 15.776 32676 Z= 0.493 Chirality : 0.051 0.319 3740 Planarity : 0.005 0.073 4183 Dihedral : 6.325 171.494 3212 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.75 % Favored : 89.46 % Rotamer: Outliers : 3.96 % Allowed : 29.14 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.87 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 2883 helix: 0.18 (0.16), residues: 1048 sheet: -1.80 (0.25), residues: 397 loop : -2.13 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 494 TYR 0.031 0.002 TYR 7 203 PHE 0.045 0.002 PHE 5 90 TRP 0.035 0.002 TRP C 111 HIS 0.013 0.001 HIS 4 386 Details of bonding type rmsd covalent geometry : bond 0.00383 (24159) covalent geometry : angle 0.98726 (32674) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.34858 ( 2) hydrogen bonds : bond 0.03576 ( 799) hydrogen bonds : angle 5.06804 ( 2247) metal coordination : bond 0.00037 ( 2) Misc. bond : bond 0.00637 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 560 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 289 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (mm) REVERT: 2 444 PHE cc_start: 0.8826 (m-80) cc_final: 0.8562 (m-80) REVERT: 3 179 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8905 (tt) REVERT: 3 193 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7789 (ttm-80) REVERT: 3 233 THR cc_start: 0.6404 (m) cc_final: 0.6106 (p) REVERT: 4 278 ASP cc_start: 0.7227 (m-30) cc_final: 0.6933 (m-30) REVERT: 4 356 MET cc_start: 0.8434 (ppp) cc_final: 0.8183 (ppp) REVERT: 4 371 CYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5031 (t) REVERT: 4 386 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7750 (m170) REVERT: 4 417 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6314 (pt) REVERT: 5 51 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6952 (ttt90) REVERT: 5 77 LYS cc_start: 0.8705 (tppt) cc_final: 0.8432 (tptm) REVERT: 5 99 LYS cc_start: 0.8823 (tppt) cc_final: 0.8419 (mptt) REVERT: 6 143 MET cc_start: 0.7641 (tpt) cc_final: 0.7396 (tpt) REVERT: 6 147 ASP cc_start: 0.4480 (m-30) cc_final: 0.3458 (t0) REVERT: 6 168 MET cc_start: 0.8912 (mmm) cc_final: 0.8404 (mmm) REVERT: 6 172 GLU cc_start: 0.8399 (mp0) cc_final: 0.7737 (mp0) REVERT: 6 180 PHE cc_start: 0.7696 (m-80) cc_final: 0.7316 (m-80) REVERT: 7 153 MET cc_start: 0.3981 (mmp) cc_final: 0.3299 (mmt) REVERT: 7 231 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8173 (mmmt) REVERT: 7 245 ILE cc_start: 0.7083 (mm) cc_final: 0.6860 (mm) REVERT: 7 252 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7853 (mmmm) REVERT: 7 320 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: E 142 CYS cc_start: 0.7298 (t) cc_final: 0.7041 (p) REVERT: E 339 TYR cc_start: 0.8678 (t80) cc_final: 0.8349 (t80) REVERT: E 402 GLN cc_start: 0.7870 (tp40) cc_final: 0.7477 (tm-30) REVERT: E 605 PHE cc_start: 0.8132 (m-80) cc_final: 0.7697 (m-80) REVERT: E 628 SER cc_start: 0.8937 (p) cc_final: 0.8428 (t) REVERT: D 64 MET cc_start: 0.8921 (mmm) cc_final: 0.8275 (tpp) REVERT: D 132 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7819 (tm-30) REVERT: D 202 MET cc_start: 0.6979 (tpp) cc_final: 0.6583 (tmm) REVERT: D 226 LYS cc_start: 0.8919 (tppt) cc_final: 0.8591 (tppt) REVERT: D 257 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6446 (p) REVERT: D 260 ILE cc_start: 0.8517 (tt) cc_final: 0.8306 (pt) REVERT: B 63 MET cc_start: 0.7232 (mpp) cc_final: 0.6596 (mtt) REVERT: B 105 GLU cc_start: 0.8153 (tp30) cc_final: 0.7474 (tp30) REVERT: B 132 ASP cc_start: 0.7616 (p0) cc_final: 0.7394 (p0) REVERT: A 34 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 70 CYS cc_start: 0.8624 (m) cc_final: 0.8298 (p) REVERT: A 87 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9232 (mm) REVERT: A 105 ASN cc_start: 0.6383 (t0) cc_final: 0.6172 (t0) REVERT: A 110 MET cc_start: -0.0974 (tpt) cc_final: -0.1475 (tpt) REVERT: C 113 MET cc_start: 0.7364 (mmt) cc_final: 0.7132 (mmp) REVERT: C 116 SER cc_start: 0.8579 (t) cc_final: 0.8165 (p) REVERT: C 186 ASP cc_start: 0.7701 (m-30) cc_final: 0.7479 (m-30) REVERT: C 193 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7243 (mmmt) outliers start: 106 outliers final: 85 residues processed: 630 average time/residue: 0.1562 time to fit residues: 152.8607 Evaluate side-chains 634 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 540 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 289 ILE Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 378 GLU Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 179 LEU Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 239 ASN Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 263 ASN Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 344 VAL Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 385 ILE Chi-restraints excluded: chain 4 residue 386 HIS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 51 ARG Chi-restraints excluded: chain 5 residue 142 ASN Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 93 PHE Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 TYR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain C residue 7 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 104 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 68 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 175 HIS 3 239 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN E 382 HIS E 531 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN A 175 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.137491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.110375 restraints weight = 50568.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108957 restraints weight = 29719.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110391 restraints weight = 24041.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111352 restraints weight = 19319.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111419 restraints weight = 17528.636| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.7337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24165 Z= 0.179 Angle : 0.988 15.560 32676 Z= 0.493 Chirality : 0.051 0.289 3740 Planarity : 0.006 0.068 4183 Dihedral : 6.308 171.675 3212 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.71 % Favored : 89.49 % Rotamer: Outliers : 4.00 % Allowed : 29.36 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.83 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 2883 helix: 0.30 (0.16), residues: 1039 sheet: -1.83 (0.25), residues: 403 loop : -2.15 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 386 TYR 0.027 0.002 TYR 7 203 PHE 0.063 0.002 PHE 5 90 TRP 0.035 0.002 TRP C 111 HIS 0.012 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00390 (24159) covalent geometry : angle 0.98776 (32674) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.34104 ( 2) hydrogen bonds : bond 0.03573 ( 799) hydrogen bonds : angle 5.03333 ( 2247) metal coordination : bond 0.00002 ( 2) Misc. bond : bond 0.00633 ( 3) =============================================================================== Job complete usr+sys time: 4906.43 seconds wall clock time: 85 minutes 16.91 seconds (5116.91 seconds total)