Starting phenix.real_space_refine on Tue Aug 26 16:17:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fl8_29270/08_2025/8fl8_29270.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 24788 2.51 5 N 6540 2.21 5 O 7337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38784 Number of models: 1 Model: "" Number of chains: 32 Chain: "8" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 356 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "Y" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1254 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3846 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 20, 'TRANS': 485} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3844 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 449} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 448} Chain: "G" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2032 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "K" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "M" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.10, per 1000 atoms: 0.21 Number of scatterers: 38784 At special positions: 0 Unit cell: (130.38, 151.58, 241.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 14 15.00 Mg 5 11.99 O 7337 8.00 N 6540 7.00 C 24788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9318 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 29 sheets defined 58.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain '8' and resid 9 through 29 removed outlier: 4.121A pdb=" N THR 8 14 " --> pdb=" O MET 8 10 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR 8 15 " --> pdb=" O ASN 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 47 Processing helix chain 'J' and resid 13 through 34 removed outlier: 3.585A pdb=" N PHE J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS J 29 " --> pdb=" O TYR J 25 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA J 31 " --> pdb=" O MET J 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 31 removed outlier: 4.005A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 50 removed outlier: 3.741A pdb=" N ASN Y 50 " --> pdb=" O THR Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 55 Processing helix chain 'Y' and resid 56 through 59 Processing helix chain 'Y' and resid 63 through 75 Processing helix chain 'Y' and resid 84 through 94 Processing helix chain 'Y' and resid 100 through 115 Processing helix chain 'Y' and resid 137 through 149 removed outlier: 3.783A pdb=" N LEU Y 141 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 171 removed outlier: 4.047A pdb=" N ILE Y 163 " --> pdb=" O VAL Y 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.582A pdb=" N GLU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.725A pdb=" N LEU A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.703A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 414 through 430 removed outlier: 4.081A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.798A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 488 removed outlier: 3.765A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.597A pdb=" N THR A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.774A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 106' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.001A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.786A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 4.032A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.623A pdb=" N ALA B 295 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.883A pdb=" N ARG B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 449 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 459 through 462 Processing helix chain 'B' and resid 463 through 476 Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.683A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.924A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.545A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.665A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.838A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.604A pdb=" N GLY C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 402 removed outlier: 4.051A pdb=" N GLY C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 413 through 430 removed outlier: 3.597A pdb=" N LYS C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.023A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 257 through 273 Processing helix chain 'D' and resid 284 through 296 removed outlier: 4.121A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 364 through 391 removed outlier: 4.285A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.752A pdb=" N GLY D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 478 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.876A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 removed outlier: 3.690A pdb=" N THR E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 295 removed outlier: 3.636A pdb=" N ASP E 288 " --> pdb=" O THR E 284 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.654A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.210A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.601A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 391 removed outlier: 3.639A pdb=" N TYR E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 433 through 447 removed outlier: 3.605A pdb=" N GLY E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 476 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 246 Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.918A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 4.017A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.531A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 390 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 422 removed outlier: 4.216A pdb=" N GLU F 422 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 478 Processing helix chain 'G' and resid 6 through 55 removed outlier: 4.757A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 55 " --> pdb=" O PHE G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 Processing helix chain 'G' and resid 112 through 118 Processing helix chain 'G' and resid 140 through 155 Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 184 through 189 removed outlier: 4.030A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 removed outlier: 3.543A pdb=" N LYS G 196 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 274 removed outlier: 3.567A pdb=" N ALA G 274 " --> pdb=" O ILE G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 110 removed outlier: 3.503A pdb=" N LYS H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 4.275A pdb=" N SER H 114 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 138 Processing helix chain 'I' and resid 9 through 24 Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'S' and resid 2 through 16 Processing helix chain 'S' and resid 17 through 40 removed outlier: 3.997A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 74 Proline residue: S 49 - end of helix removed outlier: 3.645A pdb=" N GLY S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 17 removed outlier: 3.888A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 40 removed outlier: 3.958A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 74 removed outlier: 4.656A pdb=" N THR T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) Proline residue: T 49 - end of helix Processing helix chain 'K' and resid 2 through 17 removed outlier: 4.021A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 40 removed outlier: 4.261A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 75 Proline residue: K 49 - end of helix removed outlier: 3.723A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.660A pdb=" N THR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 40 Processing helix chain 'L' and resid 43 through 74 Proline residue: L 49 - end of helix removed outlier: 3.991A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 16 Processing helix chain 'M' and resid 17 through 40 removed outlier: 3.944A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.936A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 Processing helix chain 'N' and resid 17 through 40 removed outlier: 4.057A pdb=" N GLY N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 72 Proline residue: N 49 - end of helix Processing helix chain 'O' and resid 2 through 16 Processing helix chain 'O' and resid 18 through 40 removed outlier: 3.624A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 72 Proline residue: O 49 - end of helix Processing helix chain 'P' and resid 2 through 16 Processing helix chain 'P' and resid 17 through 40 removed outlier: 3.850A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 Proline residue: P 49 - end of helix Processing helix chain 'Q' and resid 2 through 17 Processing helix chain 'Q' and resid 18 through 40 removed outlier: 3.835A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 71 Proline residue: Q 49 - end of helix Processing helix chain 'R' and resid 2 through 16 Processing helix chain 'R' and resid 19 through 40 Processing helix chain 'R' and resid 43 through 74 Proline residue: R 49 - end of helix Processing helix chain 'X' and resid 27 through 45 removed outlier: 3.657A pdb=" N SER X 42 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU X 43 " --> pdb=" O VAL X 39 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 removed outlier: 3.559A pdb=" N ILE X 60 " --> pdb=" O SER X 56 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 102 removed outlier: 3.978A pdb=" N ILE X 89 " --> pdb=" O TYR X 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE X 102 " --> pdb=" O ILE X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 114 Processing helix chain 'X' and resid 115 through 137 removed outlier: 3.940A pdb=" N ILE X 119 " --> pdb=" O LEU X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 146 Processing helix chain 'X' and resid 154 through 202 removed outlier: 3.821A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU X 191 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN X 202 " --> pdb=" O PHE X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 209 through 247 removed outlier: 3.616A pdb=" N ILE X 228 " --> pdb=" O PHE X 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP X 244 " --> pdb=" O SER X 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 72 Processing helix chain 'Z' and resid 75 through 99 removed outlier: 3.588A pdb=" N ASP Z 79 " --> pdb=" O PRO Z 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG Z 84 " --> pdb=" O PHE Z 80 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Z 86 " --> pdb=" O ASP Z 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Z 92 " --> pdb=" O VAL Z 88 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS Z 99 " --> pdb=" O SER Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 99 through 113 removed outlier: 3.683A pdb=" N VAL Z 103 " --> pdb=" O HIS Z 99 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU Z 113 " --> pdb=" O SER Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 132 removed outlier: 3.708A pdb=" N THR Z 119 " --> pdb=" O ASN Z 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU Z 129 " --> pdb=" O ASP Z 125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 184 removed outlier: 3.738A pdb=" N TYR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU Z 161 " --> pdb=" O TRP Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 207 removed outlier: 3.917A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN Z 195 " --> pdb=" O GLU Z 191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER Z 206 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS Z 207 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 10 removed outlier: 3.580A pdb=" N ASN 7 8 " --> pdb=" O LYS 7 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU 7 10 " --> pdb=" O ALA 7 6 " (cutoff:3.500A) Processing helix chain '7' and resid 10 through 18 removed outlier: 3.745A pdb=" N ILE 7 16 " --> pdb=" O TRP 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 26 through 47 removed outlier: 3.723A pdb=" N GLU 7 38 " --> pdb=" O LYS 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 91 through 126 removed outlier: 3.743A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 3.684A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL 7 149 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 7 150 " --> pdb=" O ASP 7 146 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 7 151 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET 7 152 " --> pdb=" O LYS 7 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 7 153 " --> pdb=" O VAL 7 149 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 14 removed outlier: 3.679A pdb=" N GLU 6 10 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 51 Processing helix chain '6' and resid 74 through 92 removed outlier: 3.793A pdb=" N TRP 6 79 " --> pdb=" O ILE 6 75 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU 6 80 " --> pdb=" O GLU 6 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 27 removed outlier: 3.628A pdb=" N ALA U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 32 removed outlier: 3.615A pdb=" N TYR U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS U 32 " --> pdb=" O VAL U 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 27 through 32' Processing helix chain 'U' and resid 48 through 55 Processing helix chain 'U' and resid 63 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.703A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 64 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 62 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 65 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.637A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR A 237 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 266 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 326 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 268 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL A 328 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 270 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLU A 330 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 36 removed outlier: 7.071A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 93 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 31 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.572A pdb=" N ALA B 266 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 171 removed outlier: 6.237A pdb=" N ILE B 169 " --> pdb=" O ILE B 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 37 removed outlier: 6.678A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB2, first strand: chain 'C' and resid 109 through 110 removed outlier: 8.920A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N HIS C 265 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR C 324 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 267 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 326 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL C 269 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 328 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP C 271 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU C 330 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 171 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.324A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.345A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 46 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN D 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY D 81 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N GLU D 38 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D 79 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LYS D 40 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N LEU D 77 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.950A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.492A pdb=" N ALA D 216 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL D 218 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL D 187 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY D 220 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.385A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.781A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.951A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 7.061A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.535A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 152 through 153 Processing sheet with id=AC4, first strand: chain 'E' and resid 250 through 251 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.309A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96 removed outlier: 7.069A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.609A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 73 through 76 removed outlier: 7.005A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR G 166 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU G 176 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.609A pdb=" N ASN G 131 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE I 43 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.501A pdb=" N SER H 25 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU H 10 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE H 74 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY H 73 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 29 through 30 2199 hydrogen bonds defined for protein. 6375 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: 7.08 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12641 1.34 - 1.46: 7063 1.46 - 1.58: 19501 1.58 - 1.70: 20 1.70 - 1.82: 184 Bond restraints: 39409 Sorted by residual: bond pdb=" CB PRO G 181 " pdb=" CG PRO G 181 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.01e+00 bond pdb=" C LEU C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.66e+00 bond pdb=" C TYR D 345 " pdb=" N PRO D 346 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.38e-02 5.25e+03 3.24e+00 bond pdb=" C LEU A 139 " pdb=" N PRO A 140 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.21e+00 bond pdb=" CA PHE B 405 " pdb=" CB PHE B 405 " ideal model delta sigma weight residual 1.528 1.550 -0.022 1.47e-02 4.63e+03 2.30e+00 ... (remaining 39404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 52461 2.33 - 4.67: 784 4.67 - 7.00: 125 7.00 - 9.34: 21 9.34 - 11.67: 7 Bond angle restraints: 53398 Sorted by residual: angle pdb=" C LEU C 412 " pdb=" N ASP C 413 " pdb=" CA ASP C 413 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C SER B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 122.97 -2.73 6.30e-01 2.52e+00 1.87e+01 angle pdb=" N HIS B 454 " pdb=" CA HIS B 454 " pdb=" C HIS B 454 " ideal model delta sigma weight residual 114.62 109.72 4.90 1.14e+00 7.69e-01 1.84e+01 angle pdb=" CA PRO G 181 " pdb=" N PRO G 181 " pdb=" CD PRO G 181 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 ... (remaining 53393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 22672 25.75 - 51.51: 1053 51.51 - 77.26: 122 77.26 - 103.01: 18 103.01 - 128.77: 1 Dihedral angle restraints: 23866 sinusoidal: 9350 harmonic: 14516 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.77 -128.77 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CA GLY D 426 " pdb=" C GLY D 426 " pdb=" N ILE D 427 " pdb=" CA ILE D 427 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY D 179 " pdb=" C GLY D 179 " pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 23863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5548 0.068 - 0.136: 738 0.136 - 0.204: 29 0.204 - 0.272: 4 0.272 - 0.340: 3 Chirality restraints: 6322 Sorted by residual: chirality pdb=" CB ILE D 296 " pdb=" CA ILE D 296 " pdb=" CG1 ILE D 296 " pdb=" CG2 ILE D 296 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE 7 21 " pdb=" CA ILE 7 21 " pdb=" CG1 ILE 7 21 " pdb=" CG2 ILE 7 21 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE E 296 " pdb=" CA ILE E 296 " pdb=" CG1 ILE E 296 " pdb=" CG2 ILE E 296 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 6319 not shown) Planarity restraints: 6814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 180 " -0.046 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO G 181 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 181 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 181 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 405 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C PHE B 405 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE B 405 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 406 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 476 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C SER B 476 " -0.037 2.00e-02 2.50e+03 pdb=" O SER B 476 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 477 " 0.012 2.00e-02 2.50e+03 ... (remaining 6811 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 435 2.55 - 3.14: 33484 3.14 - 3.72: 67853 3.72 - 4.31: 89514 4.31 - 4.90: 142926 Nonbonded interactions: 334212 Sorted by model distance: nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 1.962 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 1.988 2.170 nonbonded pdb=" O2B ADP F 501 " pdb="MG MG F 502 " model vdw 1.995 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.016 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.025 2.170 ... (remaining 334207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 509 or resid 601 through 602)) selection = (chain 'B' and resid 6 through 602) selection = (chain 'C' and (resid 6 through 509 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = (chain 'F' and resid 7 through 478) } ncs_group { reference = (chain 'K' and resid 1 through 74) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 74) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.290 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 39409 Z= 0.153 Angle : 0.724 11.674 53398 Z= 0.391 Chirality : 0.044 0.340 6322 Planarity : 0.004 0.067 6814 Dihedral : 14.243 128.768 14548 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 0.05 % Allowed : 0.51 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.12), residues: 5042 helix: 0.71 (0.10), residues: 2662 sheet: -0.92 (0.24), residues: 487 loop : -1.60 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 244 TYR 0.036 0.001 TYR Z 72 PHE 0.030 0.001 PHE Y 108 TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS Y 115 Details of bonding type rmsd covalent geometry : bond 0.00305 (39409) covalent geometry : angle 0.72422 (53398) hydrogen bonds : bond 0.17774 ( 2199) hydrogen bonds : angle 6.63656 ( 6375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 641 time to evaluate : 1.489 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 11 ARG cc_start: 0.8194 (mmp80) cc_final: 0.7867 (mmp-170) REVERT: Y 97 ARG cc_start: 0.8018 (tpm170) cc_final: 0.7530 (tpm170) REVERT: Y 101 PHE cc_start: 0.8591 (m-10) cc_final: 0.8193 (m-10) REVERT: Y 112 ASN cc_start: 0.8255 (m-40) cc_final: 0.8045 (m-40) REVERT: A 67 ASN cc_start: 0.8466 (t0) cc_final: 0.8095 (t0) REVERT: A 183 ASP cc_start: 0.9185 (m-30) cc_final: 0.8900 (m-30) REVERT: A 271 ASP cc_start: 0.7682 (t70) cc_final: 0.6429 (t0) REVERT: A 272 ASP cc_start: 0.8469 (m-30) cc_final: 0.7714 (m-30) REVERT: A 351 GLN cc_start: 0.9547 (pm20) cc_final: 0.9308 (pm20) REVERT: B 228 MET cc_start: 0.8688 (ppp) cc_final: 0.8234 (tpp) REVERT: B 275 LYS cc_start: 0.9592 (mtmt) cc_final: 0.9133 (mtmm) REVERT: B 378 SER cc_start: 0.8911 (t) cc_final: 0.8519 (p) REVERT: B 399 TYR cc_start: 0.8929 (m-80) cc_final: 0.8727 (m-80) REVERT: C 276 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 307 LEU cc_start: 0.9832 (tp) cc_final: 0.9434 (tp) REVERT: D 173 ASN cc_start: 0.9338 (m-40) cc_final: 0.9106 (m-40) REVERT: D 197 LEU cc_start: 0.9829 (tt) cc_final: 0.9544 (tt) REVERT: D 201 MET cc_start: 0.9584 (mmp) cc_final: 0.9172 (mmm) REVERT: D 222 MET cc_start: 0.8929 (mtp) cc_final: 0.8369 (mpp) REVERT: D 237 LEU cc_start: 0.9831 (tp) cc_final: 0.9609 (tp) REVERT: D 257 ASN cc_start: 0.9223 (t0) cc_final: 0.8841 (t0) REVERT: D 271 LEU cc_start: 0.9782 (mt) cc_final: 0.9526 (mt) REVERT: D 393 MET cc_start: 0.9130 (tpt) cc_final: 0.8748 (tpp) REVERT: D 459 MET cc_start: 0.9149 (mmp) cc_final: 0.8737 (mmm) REVERT: E 201 MET cc_start: 0.9245 (mtm) cc_final: 0.8937 (mtm) REVERT: E 257 ASN cc_start: 0.9033 (t0) cc_final: 0.8644 (t0) REVERT: E 458 TYR cc_start: 0.9276 (t80) cc_final: 0.9026 (t80) REVERT: E 459 MET cc_start: 0.9112 (mmp) cc_final: 0.8906 (mmm) REVERT: F 64 MET cc_start: 0.9107 (mmp) cc_final: 0.8674 (mmp) REVERT: F 97 ASN cc_start: 0.8576 (m110) cc_final: 0.8024 (m110) REVERT: F 201 MET cc_start: 0.9651 (mmp) cc_final: 0.9207 (mmp) REVERT: F 257 ASN cc_start: 0.9432 (m110) cc_final: 0.9004 (m110) REVERT: F 459 MET cc_start: 0.8963 (mmm) cc_final: 0.8660 (mmm) REVERT: G 49 GLN cc_start: 0.8074 (mm110) cc_final: 0.7808 (mm110) REVERT: G 102 GLN cc_start: 0.9321 (mp10) cc_final: 0.8989 (mp10) REVERT: G 154 MET cc_start: 0.9114 (mpp) cc_final: 0.8640 (mpp) REVERT: H 70 ILE cc_start: 0.6487 (tt) cc_final: 0.6261 (tt) REVERT: S 1 MET cc_start: 0.7313 (ppp) cc_final: 0.7054 (ppp) REVERT: S 50 MET cc_start: 0.7425 (pmm) cc_final: 0.7020 (pmm) REVERT: S 70 PHE cc_start: 0.9389 (m-80) cc_final: 0.9096 (t80) REVERT: T 9 TYR cc_start: 0.6159 (m-80) cc_final: 0.5883 (m-80) REVERT: T 67 MET cc_start: 0.6347 (tpt) cc_final: 0.5877 (tpp) REVERT: R 61 THR cc_start: 0.6892 (p) cc_final: 0.6595 (p) REVERT: X 88 MET cc_start: 0.8588 (mpp) cc_final: 0.6937 (mpp) REVERT: X 162 GLU cc_start: 0.9457 (mm-30) cc_final: 0.8883 (mt-10) REVERT: 6 16 LEU cc_start: 0.9360 (mm) cc_final: 0.8839 (pp) REVERT: 6 90 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6838 (mm-30) REVERT: U 28 VAL cc_start: 0.8200 (t) cc_final: 0.7627 (t) REVERT: U 48 LEU cc_start: 0.9047 (mt) cc_final: 0.8843 (pt) outliers start: 2 outliers final: 0 residues processed: 641 average time/residue: 0.2247 time to fit residues: 234.4695 Evaluate side-chains 431 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 20.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 112 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 217 GLN C 210 GLN C 245 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN G 190 GLN G 217 GLN H 51 GLN H 78 GLN H 98 GLN H 111 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN ** 7 171 ASN ** 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 = 0.3629 r_free = 0.3629 target = 0.079547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052939 restraints weight = 209132.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053905 restraints weight = 130926.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054729 restraints weight = 88215.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055151 restraints weight = 66018.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055630 restraints weight = 54396.873| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39409 Z= 0.183 Angle : 0.660 9.927 53398 Z= 0.341 Chirality : 0.044 0.374 6322 Planarity : 0.005 0.093 6814 Dihedral : 6.963 122.639 5556 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.57 % Favored : 94.25 % Rotamer: Outliers : 0.12 % Allowed : 5.76 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 5042 helix: 0.79 (0.10), residues: 2714 sheet: -0.87 (0.24), residues: 476 loop : -1.44 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 176 TYR 0.037 0.002 TYR Z 72 PHE 0.035 0.002 PHE R 64 TRP 0.010 0.001 TRP X 126 HIS 0.008 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00392 (39409) covalent geometry : angle 0.65954 (53398) hydrogen bonds : bond 0.05033 ( 2199) hydrogen bonds : angle 5.13547 ( 6375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 581 time to evaluate : 1.545 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: symmetry clash REVERT: 8 20 MET cc_start: 0.4667 (tmm) cc_final: 0.4463 (tmm) REVERT: 8 27 PHE cc_start: 0.8038 (m-80) cc_final: 0.7780 (m-10) REVERT: Y 11 ARG cc_start: 0.8234 (mmp80) cc_final: 0.7857 (mmp-170) REVERT: Y 68 ASN cc_start: 0.9497 (m110) cc_final: 0.9285 (m110) REVERT: Y 97 ARG cc_start: 0.8239 (tpm170) cc_final: 0.7851 (tpm170) REVERT: Y 101 PHE cc_start: 0.8736 (m-10) cc_final: 0.8309 (m-10) REVERT: Y 108 PHE cc_start: 0.9299 (t80) cc_final: 0.8886 (t80) REVERT: Y 112 ASN cc_start: 0.8038 (m110) cc_final: 0.7586 (m110) REVERT: A 46 LEU cc_start: 0.9763 (mt) cc_final: 0.9527 (mt) REVERT: A 67 ASN cc_start: 0.8295 (t0) cc_final: 0.7927 (t0) REVERT: A 183 ASP cc_start: 0.8956 (m-30) cc_final: 0.8658 (m-30) REVERT: A 272 ASP cc_start: 0.8428 (m-30) cc_final: 0.8063 (m-30) REVERT: A 351 GLN cc_start: 0.9499 (pm20) cc_final: 0.9224 (pm20) REVERT: B 208 VAL cc_start: 0.9722 (m) cc_final: 0.9006 (m) REVERT: B 218 LEU cc_start: 0.9701 (tp) cc_final: 0.9454 (tt) REVERT: B 228 MET cc_start: 0.8755 (ppp) cc_final: 0.8219 (tpp) REVERT: B 272 ASP cc_start: 0.8729 (t70) cc_final: 0.8308 (t0) REVERT: B 275 LYS cc_start: 0.9678 (mtmt) cc_final: 0.9171 (mtmt) REVERT: B 371 LEU cc_start: 0.9658 (mt) cc_final: 0.9219 (tt) REVERT: B 378 SER cc_start: 0.8918 (t) cc_final: 0.8269 (p) REVERT: C 307 LEU cc_start: 0.9792 (tp) cc_final: 0.9227 (tp) REVERT: D 197 LEU cc_start: 0.9838 (tt) cc_final: 0.9580 (tt) REVERT: D 201 MET cc_start: 0.9559 (mmp) cc_final: 0.9110 (mmm) REVERT: D 237 LEU cc_start: 0.9815 (tp) cc_final: 0.9537 (tp) REVERT: D 257 ASN cc_start: 0.9209 (t0) cc_final: 0.8750 (t0) REVERT: D 271 LEU cc_start: 0.9596 (mt) cc_final: 0.9324 (mt) REVERT: D 459 MET cc_start: 0.9170 (mmp) cc_final: 0.8683 (mmm) REVERT: E 257 ASN cc_start: 0.8986 (t0) cc_final: 0.8518 (t0) REVERT: E 288 ASP cc_start: 0.9267 (m-30) cc_final: 0.9035 (m-30) REVERT: F 64 MET cc_start: 0.9091 (mmp) cc_final: 0.8639 (mmp) REVERT: F 97 ASN cc_start: 0.8446 (m110) cc_final: 0.7975 (m110) REVERT: F 201 MET cc_start: 0.9540 (mmp) cc_final: 0.9165 (mmm) REVERT: F 257 ASN cc_start: 0.9526 (m110) cc_final: 0.9198 (m110) REVERT: F 459 MET cc_start: 0.9051 (mmm) cc_final: 0.8330 (mmm) REVERT: G 49 GLN cc_start: 0.8231 (mm110) cc_final: 0.7770 (mm-40) REVERT: G 154 MET cc_start: 0.9234 (mpp) cc_final: 0.8799 (mpp) REVERT: S 1 MET cc_start: 0.7519 (ppp) cc_final: 0.7275 (ppp) REVERT: S 70 PHE cc_start: 0.9385 (m-80) cc_final: 0.9179 (t80) REVERT: K 1 MET cc_start: 0.6730 (pmm) cc_final: 0.5727 (ppp) REVERT: X 88 MET cc_start: 0.8956 (mpp) cc_final: 0.8710 (mpp) REVERT: X 135 TYR cc_start: 0.9321 (t80) cc_final: 0.8853 (t80) REVERT: X 162 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9102 (tt0) REVERT: X 176 ARG cc_start: 0.8392 (pmt-80) cc_final: 0.8158 (pmt-80) REVERT: Z 85 MET cc_start: 0.7833 (pmm) cc_final: 0.7494 (pmm) REVERT: 6 16 LEU cc_start: 0.9351 (mm) cc_final: 0.8956 (pp) REVERT: 6 90 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7568 (mm-30) REVERT: U 48 LEU cc_start: 0.9025 (mt) cc_final: 0.8661 (pt) outliers start: 5 outliers final: 1 residues processed: 586 average time/residue: 0.2145 time to fit residues: 206.6573 Evaluate side-chains 415 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 308 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 464 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.080105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053880 restraints weight = 210757.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054021 restraints weight = 126060.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055195 restraints weight = 91773.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055295 restraints weight = 65506.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055413 restraints weight = 61436.322| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39409 Z= 0.138 Angle : 0.643 10.471 53398 Z= 0.326 Chirality : 0.045 0.379 6322 Planarity : 0.004 0.073 6814 Dihedral : 6.790 115.945 5556 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.12), residues: 5042 helix: 0.75 (0.10), residues: 2703 sheet: -0.80 (0.24), residues: 488 loop : -1.46 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 39 TYR 0.032 0.001 TYR Z 72 PHE 0.027 0.002 PHE R 70 TRP 0.031 0.002 TRP X 126 HIS 0.010 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00293 (39409) covalent geometry : angle 0.64298 (53398) hydrogen bonds : bond 0.04613 ( 2199) hydrogen bonds : angle 4.93052 ( 6375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.091 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: 8 20 MET cc_start: 0.4652 (tmm) cc_final: 0.4431 (tmm) REVERT: 8 27 PHE cc_start: 0.8172 (m-80) cc_final: 0.7841 (m-10) REVERT: Y 11 ARG cc_start: 0.8227 (mmp80) cc_final: 0.7982 (mmp-170) REVERT: Y 97 ARG cc_start: 0.8081 (tpm170) cc_final: 0.7817 (tpm170) REVERT: Y 101 PHE cc_start: 0.8786 (m-10) cc_final: 0.8332 (m-10) REVERT: Y 108 PHE cc_start: 0.9293 (t80) cc_final: 0.8873 (t80) REVERT: Y 112 ASN cc_start: 0.8070 (m110) cc_final: 0.7630 (m110) REVERT: A 46 LEU cc_start: 0.9753 (mt) cc_final: 0.9515 (mt) REVERT: A 67 ASN cc_start: 0.8399 (t0) cc_final: 0.8021 (t0) REVERT: A 183 ASP cc_start: 0.8906 (m-30) cc_final: 0.8611 (m-30) REVERT: A 270 TYR cc_start: 0.9237 (m-80) cc_final: 0.8775 (m-10) REVERT: A 272 ASP cc_start: 0.8417 (m-30) cc_final: 0.7971 (m-30) REVERT: A 351 GLN cc_start: 0.9466 (pm20) cc_final: 0.9218 (pm20) REVERT: A 357 GLU cc_start: 0.9305 (tp30) cc_final: 0.9031 (tp30) REVERT: B 56 GLU cc_start: 0.8714 (mp0) cc_final: 0.8482 (mp0) REVERT: B 228 MET cc_start: 0.8661 (ppp) cc_final: 0.8176 (tpp) REVERT: B 275 LYS cc_start: 0.9679 (mtmt) cc_final: 0.9338 (mtmm) REVERT: B 378 SER cc_start: 0.8528 (t) cc_final: 0.8308 (p) REVERT: C 276 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8772 (tm-30) REVERT: C 307 LEU cc_start: 0.9777 (tp) cc_final: 0.9311 (tp) REVERT: D 197 LEU cc_start: 0.9844 (tt) cc_final: 0.9596 (tt) REVERT: D 201 MET cc_start: 0.9557 (mmp) cc_final: 0.9086 (mmm) REVERT: D 237 LEU cc_start: 0.9776 (tp) cc_final: 0.9478 (tp) REVERT: D 257 ASN cc_start: 0.9131 (t0) cc_final: 0.8588 (t0) REVERT: D 263 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 271 LEU cc_start: 0.9575 (mt) cc_final: 0.9284 (mt) REVERT: D 393 MET cc_start: 0.9021 (tpt) cc_final: 0.8549 (tpp) REVERT: D 459 MET cc_start: 0.9141 (mmp) cc_final: 0.8646 (mmm) REVERT: E 257 ASN cc_start: 0.8987 (t0) cc_final: 0.8594 (t0) REVERT: E 288 ASP cc_start: 0.9236 (m-30) cc_final: 0.8984 (m-30) REVERT: F 64 MET cc_start: 0.9146 (mmp) cc_final: 0.8661 (mmp) REVERT: F 97 ASN cc_start: 0.8601 (m110) cc_final: 0.8202 (m110) REVERT: F 134 LEU cc_start: 0.9452 (mt) cc_final: 0.9130 (mt) REVERT: F 257 ASN cc_start: 0.9519 (m110) cc_final: 0.7907 (m110) REVERT: F 388 ILE cc_start: 0.9631 (mm) cc_final: 0.9380 (pt) REVERT: F 459 MET cc_start: 0.9037 (mmm) cc_final: 0.8520 (mmm) REVERT: G 102 GLN cc_start: 0.9290 (mp10) cc_final: 0.9049 (mp-120) REVERT: G 154 MET cc_start: 0.9249 (mpp) cc_final: 0.8795 (mpp) REVERT: I 14 LEU cc_start: 0.9344 (tp) cc_final: 0.9124 (mm) REVERT: T 1 MET cc_start: 0.9532 (mpp) cc_final: 0.9222 (mmp) REVERT: T 48 PHE cc_start: 0.7339 (m-10) cc_final: 0.6882 (m-10) REVERT: L 1 MET cc_start: 0.7453 (mmp) cc_final: 0.7215 (mmp) REVERT: N 26 ILE cc_start: 0.7000 (mm) cc_final: 0.6609 (mm) REVERT: Q 50 MET cc_start: 0.2053 (mmm) cc_final: 0.1243 (mmm) REVERT: R 50 MET cc_start: 0.3041 (mpp) cc_final: 0.2759 (mmm) REVERT: X 88 MET cc_start: 0.9008 (mpp) cc_final: 0.8762 (mpp) REVERT: X 135 TYR cc_start: 0.9307 (t80) cc_final: 0.8849 (t80) REVERT: X 220 MET cc_start: 0.8909 (ppp) cc_final: 0.8625 (ppp) REVERT: Z 85 MET cc_start: 0.7675 (pmm) cc_final: 0.7427 (pmm) REVERT: 6 90 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7431 (mm-30) REVERT: U 48 LEU cc_start: 0.9045 (mt) cc_final: 0.8734 (pp) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.2191 time to fit residues: 210.9630 Evaluate side-chains 416 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 385 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 477 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 427 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 95 ASN A 145 HIS A 245 GLN A 407 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 263 GLN F 35 ASN F 257 ASN G 49 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.077085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.051276 restraints weight = 213439.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.051487 restraints weight = 128862.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052506 restraints weight = 88912.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052550 restraints weight = 69002.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052672 restraints weight = 61091.645| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 39409 Z= 0.225 Angle : 0.690 11.030 53398 Z= 0.354 Chirality : 0.045 0.365 6322 Planarity : 0.005 0.054 6814 Dihedral : 6.645 113.648 5556 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.12), residues: 5042 helix: 0.76 (0.10), residues: 2659 sheet: -0.90 (0.23), residues: 517 loop : -1.34 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 169 TYR 0.028 0.002 TYR X 241 PHE 0.041 0.002 PHE R 64 TRP 0.010 0.001 TRP 6 79 HIS 0.008 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00484 (39409) covalent geometry : angle 0.69021 (53398) hydrogen bonds : bond 0.04567 ( 2199) hydrogen bonds : angle 4.90822 ( 6375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 531 time to evaluate : 1.434 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: 8 27 PHE cc_start: 0.8263 (m-80) cc_final: 0.7918 (m-10) REVERT: Y 97 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8198 (tpm170) REVERT: Y 103 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9286 (tptm) REVERT: Y 108 PHE cc_start: 0.9322 (t80) cc_final: 0.8882 (t80) REVERT: Y 112 ASN cc_start: 0.8170 (m110) cc_final: 0.7651 (m-40) REVERT: A 67 ASN cc_start: 0.8464 (t0) cc_final: 0.8143 (t0) REVERT: A 183 ASP cc_start: 0.8944 (m-30) cc_final: 0.8676 (m-30) REVERT: A 270 TYR cc_start: 0.9323 (m-80) cc_final: 0.9058 (m-10) REVERT: A 351 GLN cc_start: 0.9508 (pm20) cc_final: 0.9257 (pm20) REVERT: A 357 GLU cc_start: 0.9296 (tp30) cc_final: 0.9006 (tp30) REVERT: B 56 GLU cc_start: 0.8673 (mp0) cc_final: 0.8453 (mp0) REVERT: B 64 MET cc_start: 0.9497 (ttt) cc_final: 0.9163 (tpp) REVERT: B 183 ASP cc_start: 0.9303 (m-30) cc_final: 0.8802 (m-30) REVERT: B 228 MET cc_start: 0.8699 (ppp) cc_final: 0.7928 (tpp) REVERT: B 272 ASP cc_start: 0.8732 (t70) cc_final: 0.8481 (t0) REVERT: B 275 LYS cc_start: 0.9716 (mtmt) cc_final: 0.9400 (mtmm) REVERT: B 371 LEU cc_start: 0.9715 (mt) cc_final: 0.9259 (tt) REVERT: B 378 SER cc_start: 0.9003 (t) cc_final: 0.8760 (p) REVERT: C 69 GLU cc_start: 0.8615 (mp0) cc_final: 0.8289 (mp0) REVERT: C 270 TYR cc_start: 0.8879 (m-10) cc_final: 0.8369 (m-10) REVERT: C 307 LEU cc_start: 0.9745 (tp) cc_final: 0.9512 (tp) REVERT: D 197 LEU cc_start: 0.9829 (tt) cc_final: 0.9572 (tt) REVERT: D 201 MET cc_start: 0.9588 (mmp) cc_final: 0.9148 (mmm) REVERT: D 237 LEU cc_start: 0.9789 (tp) cc_final: 0.9492 (tp) REVERT: D 257 ASN cc_start: 0.9191 (t0) cc_final: 0.8624 (t0) REVERT: D 271 LEU cc_start: 0.9604 (mt) cc_final: 0.9240 (mt) REVERT: D 459 MET cc_start: 0.9155 (mmp) cc_final: 0.8509 (mmm) REVERT: E 257 ASN cc_start: 0.9174 (t0) cc_final: 0.8616 (t0) REVERT: E 288 ASP cc_start: 0.9248 (m-30) cc_final: 0.8995 (m-30) REVERT: E 353 SER cc_start: 0.9584 (m) cc_final: 0.9238 (t) REVERT: F 64 MET cc_start: 0.9175 (mmp) cc_final: 0.8660 (mmp) REVERT: F 97 ASN cc_start: 0.8420 (m110) cc_final: 0.7944 (m110) REVERT: F 117 ILE cc_start: 0.9712 (pt) cc_final: 0.9253 (mm) REVERT: F 134 LEU cc_start: 0.9454 (mt) cc_final: 0.9113 (mt) REVERT: F 201 MET cc_start: 0.9396 (mmm) cc_final: 0.9136 (mpp) REVERT: F 257 ASN cc_start: 0.9119 (m-40) cc_final: 0.8775 (t0) REVERT: F 388 ILE cc_start: 0.9681 (mm) cc_final: 0.9444 (pt) REVERT: G 154 MET cc_start: 0.9366 (mpp) cc_final: 0.8830 (mpp) REVERT: T 1 MET cc_start: 0.9501 (mpp) cc_final: 0.9189 (mmp) REVERT: T 48 PHE cc_start: 0.7409 (m-10) cc_final: 0.6953 (m-10) REVERT: Q 39 ARG cc_start: 0.9099 (ptm160) cc_final: 0.8746 (ptt180) REVERT: X 135 TYR cc_start: 0.9325 (t80) cc_final: 0.8887 (t80) REVERT: X 220 MET cc_start: 0.9008 (ppp) cc_final: 0.8758 (ppp) REVERT: Z 90 ASP cc_start: 0.9090 (m-30) cc_final: 0.8763 (m-30) REVERT: Z 148 HIS cc_start: 0.9213 (m-70) cc_final: 0.9011 (m-70) REVERT: 6 90 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6973 (mm-30) REVERT: U 48 LEU cc_start: 0.9155 (mt) cc_final: 0.8786 (pt) outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.2089 time to fit residues: 182.4502 Evaluate side-chains 385 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 440 optimal weight: 7.9990 chunk 454 optimal weight: 30.0000 chunk 400 optimal weight: 8.9990 chunk 468 optimal weight: 8.9990 chunk 395 optimal weight: 8.9990 chunk 442 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 436 optimal weight: 30.0000 chunk 278 optimal weight: 0.0980 chunk 176 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.076622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.051099 restraints weight = 216236.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051156 restraints weight = 129933.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051852 restraints weight = 96763.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052166 restraints weight = 72231.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052239 restraints weight = 62997.273| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 39409 Z= 0.211 Angle : 0.678 9.815 53398 Z= 0.347 Chirality : 0.045 0.381 6322 Planarity : 0.004 0.071 6814 Dihedral : 6.557 111.683 5556 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.12), residues: 5042 helix: 0.74 (0.10), residues: 2716 sheet: -0.81 (0.23), residues: 516 loop : -1.36 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 8 37 TYR 0.024 0.002 TYR Z 72 PHE 0.050 0.002 PHE R 70 TRP 0.010 0.001 TRP 6 79 HIS 0.008 0.001 HIS G 122 Details of bonding type rmsd covalent geometry : bond 0.00454 (39409) covalent geometry : angle 0.67826 (53398) hydrogen bonds : bond 0.04492 ( 2199) hydrogen bonds : angle 4.88180 ( 6375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 1.289 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: 8 27 PHE cc_start: 0.8290 (m-10) cc_final: 0.7897 (m-10) REVERT: J 24 TYR cc_start: 0.3621 (m-80) cc_final: 0.3388 (m-10) REVERT: Y 97 ARG cc_start: 0.8620 (tpm170) cc_final: 0.8296 (tpm170) REVERT: Y 103 LYS cc_start: 0.9568 (tmtt) cc_final: 0.9307 (tptm) REVERT: Y 108 PHE cc_start: 0.9326 (t80) cc_final: 0.8888 (t80) REVERT: Y 112 ASN cc_start: 0.8125 (m110) cc_final: 0.7594 (m-40) REVERT: A 67 ASN cc_start: 0.8337 (t0) cc_final: 0.7993 (t0) REVERT: A 183 ASP cc_start: 0.8945 (m-30) cc_final: 0.8700 (m-30) REVERT: A 270 TYR cc_start: 0.9345 (m-80) cc_final: 0.9103 (m-10) REVERT: A 351 GLN cc_start: 0.9496 (pm20) cc_final: 0.9259 (pm20) REVERT: A 357 GLU cc_start: 0.9304 (tp30) cc_final: 0.9040 (tp30) REVERT: B 17 ARG cc_start: 0.9016 (mpp-170) cc_final: 0.8790 (ptt-90) REVERT: B 56 GLU cc_start: 0.8679 (mp0) cc_final: 0.8428 (mp0) REVERT: B 183 ASP cc_start: 0.9321 (m-30) cc_final: 0.8841 (m-30) REVERT: B 228 MET cc_start: 0.8722 (ppp) cc_final: 0.8000 (tpp) REVERT: B 272 ASP cc_start: 0.8727 (t70) cc_final: 0.8422 (t0) REVERT: B 275 LYS cc_start: 0.9722 (mtmt) cc_final: 0.9393 (mtmm) REVERT: B 361 LYS cc_start: 0.9509 (mmmt) cc_final: 0.9261 (mmmt) REVERT: B 371 LEU cc_start: 0.9745 (mt) cc_final: 0.9266 (tt) REVERT: B 378 SER cc_start: 0.8951 (t) cc_final: 0.8694 (p) REVERT: B 399 TYR cc_start: 0.8778 (m-80) cc_final: 0.8527 (m-80) REVERT: C 270 TYR cc_start: 0.8939 (m-10) cc_final: 0.8481 (m-10) REVERT: C 307 LEU cc_start: 0.9755 (tp) cc_final: 0.9555 (tp) REVERT: D 197 LEU cc_start: 0.9821 (tt) cc_final: 0.9577 (tt) REVERT: D 201 MET cc_start: 0.9589 (mmp) cc_final: 0.9130 (mmm) REVERT: D 237 LEU cc_start: 0.9784 (tp) cc_final: 0.9496 (tp) REVERT: D 257 ASN cc_start: 0.9187 (t0) cc_final: 0.8618 (t0) REVERT: D 271 LEU cc_start: 0.9583 (mt) cc_final: 0.9284 (mt) REVERT: D 459 MET cc_start: 0.9169 (mmp) cc_final: 0.8544 (mmm) REVERT: E 74 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8353 (mt-10) REVERT: E 257 ASN cc_start: 0.9205 (t0) cc_final: 0.8646 (t0) REVERT: E 288 ASP cc_start: 0.9252 (m-30) cc_final: 0.9000 (m-30) REVERT: E 353 SER cc_start: 0.9608 (m) cc_final: 0.9287 (t) REVERT: F 64 MET cc_start: 0.9201 (mmp) cc_final: 0.8650 (mmp) REVERT: F 97 ASN cc_start: 0.8555 (m110) cc_final: 0.8164 (m110) REVERT: F 134 LEU cc_start: 0.9473 (mt) cc_final: 0.9148 (mt) REVERT: F 257 ASN cc_start: 0.9132 (m-40) cc_final: 0.8720 (t0) REVERT: F 388 ILE cc_start: 0.9702 (mm) cc_final: 0.9491 (pt) REVERT: G 102 GLN cc_start: 0.9566 (mm110) cc_final: 0.9294 (mp-120) REVERT: G 154 MET cc_start: 0.9465 (mpp) cc_final: 0.8938 (mpp) REVERT: T 1 MET cc_start: 0.9495 (mpp) cc_final: 0.9192 (mmp) REVERT: Q 50 MET cc_start: 0.2097 (mmm) cc_final: 0.1494 (mmm) REVERT: X 135 TYR cc_start: 0.9328 (t80) cc_final: 0.8894 (t80) REVERT: X 220 MET cc_start: 0.9126 (ppp) cc_final: 0.8880 (ppp) REVERT: Z 93 ASN cc_start: 0.9148 (t0) cc_final: 0.8907 (m110) REVERT: Z 148 HIS cc_start: 0.9196 (m-70) cc_final: 0.8982 (m-70) REVERT: 7 161 PRO cc_start: 0.7678 (Cg_endo) cc_final: 0.7457 (Cg_exo) REVERT: 6 90 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6919 (mm-30) REVERT: U 48 LEU cc_start: 0.9151 (mt) cc_final: 0.8815 (pt) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.2024 time to fit residues: 172.8049 Evaluate side-chains 389 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 452 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 288 optimal weight: 10.0000 chunk 396 optimal weight: 30.0000 chunk 393 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 323 optimal weight: 30.0000 chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.076296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050642 restraints weight = 215397.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050510 restraints weight = 132873.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.051326 restraints weight = 94072.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051588 restraints weight = 73613.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051678 restraints weight = 68758.234| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39409 Z= 0.188 Angle : 0.669 9.729 53398 Z= 0.342 Chirality : 0.045 0.394 6322 Planarity : 0.004 0.059 6814 Dihedral : 6.513 111.686 5556 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.89 % Rotamer: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.12), residues: 5042 helix: 0.79 (0.10), residues: 2666 sheet: -0.68 (0.24), residues: 505 loop : -1.25 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 40 TYR 0.028 0.002 TYR X 247 PHE 0.041 0.002 PHE R 64 TRP 0.011 0.001 TRP X 126 HIS 0.005 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00410 (39409) covalent geometry : angle 0.66935 (53398) hydrogen bonds : bond 0.04400 ( 2199) hydrogen bonds : angle 4.80022 ( 6375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 514 time to evaluate : 1.038 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: 8 27 PHE cc_start: 0.8237 (m-10) cc_final: 0.7843 (m-10) REVERT: Y 97 ARG cc_start: 0.8724 (tpm170) cc_final: 0.8336 (tpm170) REVERT: Y 107 ASP cc_start: 0.9539 (m-30) cc_final: 0.9309 (m-30) REVERT: Y 108 PHE cc_start: 0.9319 (t80) cc_final: 0.8920 (t80) REVERT: Y 112 ASN cc_start: 0.8087 (m110) cc_final: 0.7555 (m110) REVERT: A 67 ASN cc_start: 0.8333 (t0) cc_final: 0.8002 (t0) REVERT: A 183 ASP cc_start: 0.8947 (m-30) cc_final: 0.8715 (m-30) REVERT: A 270 TYR cc_start: 0.9360 (m-80) cc_final: 0.9125 (m-10) REVERT: A 294 GLU cc_start: 0.8723 (pt0) cc_final: 0.8415 (pt0) REVERT: A 351 GLN cc_start: 0.9491 (pm20) cc_final: 0.9250 (pm20) REVERT: A 357 GLU cc_start: 0.9310 (tp30) cc_final: 0.9044 (tp30) REVERT: B 56 GLU cc_start: 0.8694 (mp0) cc_final: 0.8422 (mp0) REVERT: B 64 MET cc_start: 0.9569 (ttm) cc_final: 0.9153 (tpp) REVERT: B 183 ASP cc_start: 0.9282 (m-30) cc_final: 0.8882 (m-30) REVERT: B 226 ASP cc_start: 0.8898 (t0) cc_final: 0.8346 (t0) REVERT: B 228 MET cc_start: 0.8777 (ppp) cc_final: 0.8040 (tpp) REVERT: B 275 LYS cc_start: 0.9711 (mtmt) cc_final: 0.9477 (mtmt) REVERT: B 357 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 361 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9354 (mmmt) REVERT: B 371 LEU cc_start: 0.9737 (mt) cc_final: 0.9248 (tt) REVERT: B 378 SER cc_start: 0.8966 (t) cc_final: 0.8678 (p) REVERT: B 399 TYR cc_start: 0.8826 (m-80) cc_final: 0.8547 (m-80) REVERT: B 470 PHE cc_start: 0.9552 (t80) cc_final: 0.9244 (t80) REVERT: B 471 LEU cc_start: 0.9650 (tt) cc_final: 0.9368 (pp) REVERT: C 270 TYR cc_start: 0.8948 (m-10) cc_final: 0.8490 (m-10) REVERT: C 307 LEU cc_start: 0.9763 (tp) cc_final: 0.9560 (tp) REVERT: D 197 LEU cc_start: 0.9820 (tt) cc_final: 0.9603 (tt) REVERT: D 201 MET cc_start: 0.9558 (mmp) cc_final: 0.9147 (mmm) REVERT: D 237 LEU cc_start: 0.9785 (tp) cc_final: 0.9485 (tp) REVERT: D 257 ASN cc_start: 0.9222 (t0) cc_final: 0.8629 (t0) REVERT: D 271 LEU cc_start: 0.9564 (mt) cc_final: 0.9260 (mt) REVERT: D 393 MET cc_start: 0.9217 (tpt) cc_final: 0.8837 (tpp) REVERT: D 459 MET cc_start: 0.9125 (mmp) cc_final: 0.8497 (mmm) REVERT: E 74 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8370 (mt-10) REVERT: E 257 ASN cc_start: 0.9213 (t0) cc_final: 0.8659 (t0) REVERT: E 288 ASP cc_start: 0.9249 (m-30) cc_final: 0.9001 (m-30) REVERT: F 64 MET cc_start: 0.9018 (mmp) cc_final: 0.8511 (mmp) REVERT: F 97 ASN cc_start: 0.8732 (m110) cc_final: 0.8368 (m110) REVERT: F 134 LEU cc_start: 0.9452 (mt) cc_final: 0.9104 (mt) REVERT: F 201 MET cc_start: 0.9390 (mpp) cc_final: 0.8979 (mpp) REVERT: F 257 ASN cc_start: 0.9240 (m-40) cc_final: 0.8564 (m110) REVERT: F 308 GLN cc_start: 0.9108 (pm20) cc_final: 0.8862 (pm20) REVERT: F 388 ILE cc_start: 0.9693 (mm) cc_final: 0.9466 (pt) REVERT: G 154 MET cc_start: 0.9455 (mpp) cc_final: 0.8915 (mpp) REVERT: S 1 MET cc_start: 0.7696 (ppp) cc_final: 0.7378 (ppp) REVERT: T 1 MET cc_start: 0.9481 (mpp) cc_final: 0.9205 (mmp) REVERT: T 48 PHE cc_start: 0.7457 (m-10) cc_final: 0.7033 (m-10) REVERT: M 59 GLU cc_start: 0.6104 (mp0) cc_final: 0.5715 (mp0) REVERT: Q 50 MET cc_start: 0.2343 (mmm) cc_final: 0.1917 (mmm) REVERT: X 81 ASN cc_start: 0.9431 (m-40) cc_final: 0.9060 (p0) REVERT: X 88 MET cc_start: 0.9313 (mmt) cc_final: 0.9080 (mmt) REVERT: X 135 TYR cc_start: 0.9321 (t80) cc_final: 0.8896 (t80) REVERT: X 220 MET cc_start: 0.9022 (ppp) cc_final: 0.8790 (ppp) REVERT: Z 148 HIS cc_start: 0.9196 (m-70) cc_final: 0.8985 (m-70) REVERT: 6 90 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6861 (mm-30) REVERT: U 48 LEU cc_start: 0.9182 (mt) cc_final: 0.8870 (pt) outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 0.2046 time to fit residues: 174.5750 Evaluate side-chains 392 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 272 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 396 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.075813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050328 restraints weight = 214082.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050178 restraints weight = 130079.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051072 restraints weight = 97604.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051168 restraints weight = 72065.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051312 restraints weight = 64606.540| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39409 Z= 0.195 Angle : 0.690 10.913 53398 Z= 0.352 Chirality : 0.045 0.402 6322 Planarity : 0.004 0.061 6814 Dihedral : 6.489 114.512 5556 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 5042 helix: 0.76 (0.10), residues: 2656 sheet: -0.62 (0.24), residues: 505 loop : -1.25 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 17 TYR 0.023 0.002 TYR X 247 PHE 0.044 0.002 PHE R 70 TRP 0.012 0.001 TRP 6 79 HIS 0.005 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00422 (39409) covalent geometry : angle 0.69020 (53398) hydrogen bonds : bond 0.04380 ( 2199) hydrogen bonds : angle 4.89184 ( 6375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.485 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: 8 10 MET cc_start: 0.2123 (mtp) cc_final: 0.1923 (mtm) REVERT: 8 27 PHE cc_start: 0.8307 (m-10) cc_final: 0.7909 (m-10) REVERT: Y 97 ARG cc_start: 0.8713 (tpm170) cc_final: 0.8180 (tpm170) REVERT: Y 98 LEU cc_start: 0.8900 (pp) cc_final: 0.8642 (pp) REVERT: Y 108 PHE cc_start: 0.9329 (t80) cc_final: 0.8932 (t80) REVERT: Y 112 ASN cc_start: 0.8154 (m110) cc_final: 0.7588 (m-40) REVERT: A 67 ASN cc_start: 0.8320 (t0) cc_final: 0.8027 (t0) REVERT: A 183 ASP cc_start: 0.8892 (m-30) cc_final: 0.8656 (m-30) REVERT: A 203 CYS cc_start: 0.9029 (m) cc_final: 0.8760 (m) REVERT: A 270 TYR cc_start: 0.9389 (m-80) cc_final: 0.9170 (m-10) REVERT: A 351 GLN cc_start: 0.9489 (pm20) cc_final: 0.9237 (pm20) REVERT: A 357 GLU cc_start: 0.9296 (tp30) cc_final: 0.9037 (tp30) REVERT: B 17 ARG cc_start: 0.9173 (mpp-170) cc_final: 0.8921 (ptt-90) REVERT: B 56 GLU cc_start: 0.8698 (mp0) cc_final: 0.8433 (mp0) REVERT: B 183 ASP cc_start: 0.9270 (m-30) cc_final: 0.8884 (m-30) REVERT: B 226 ASP cc_start: 0.9053 (t0) cc_final: 0.8546 (t0) REVERT: B 228 MET cc_start: 0.8777 (ppp) cc_final: 0.8286 (tpp) REVERT: B 361 LYS cc_start: 0.9579 (mmmt) cc_final: 0.9361 (mmmt) REVERT: B 371 LEU cc_start: 0.9755 (mt) cc_final: 0.9266 (tt) REVERT: B 378 SER cc_start: 0.8925 (t) cc_final: 0.8664 (p) REVERT: B 399 TYR cc_start: 0.8837 (m-80) cc_final: 0.8578 (m-80) REVERT: B 470 PHE cc_start: 0.9488 (t80) cc_final: 0.9229 (t80) REVERT: C 270 TYR cc_start: 0.9007 (m-10) cc_final: 0.8556 (m-10) REVERT: C 307 LEU cc_start: 0.9785 (tp) cc_final: 0.9579 (tp) REVERT: D 201 MET cc_start: 0.9507 (mmp) cc_final: 0.9167 (mmm) REVERT: D 237 LEU cc_start: 0.9785 (tp) cc_final: 0.9503 (tp) REVERT: D 257 ASN cc_start: 0.9235 (t0) cc_final: 0.8637 (t0) REVERT: D 271 LEU cc_start: 0.9587 (mt) cc_final: 0.9274 (mt) REVERT: D 311 TYR cc_start: 0.9152 (t80) cc_final: 0.8941 (t80) REVERT: D 459 MET cc_start: 0.9094 (mmp) cc_final: 0.8466 (mmm) REVERT: E 257 ASN cc_start: 0.9258 (t0) cc_final: 0.8672 (t0) REVERT: E 288 ASP cc_start: 0.9257 (m-30) cc_final: 0.8998 (m-30) REVERT: F 64 MET cc_start: 0.9099 (mmp) cc_final: 0.8607 (mmp) REVERT: F 97 ASN cc_start: 0.8762 (m110) cc_final: 0.8387 (m110) REVERT: F 201 MET cc_start: 0.9369 (mpp) cc_final: 0.8618 (mpp) REVERT: F 257 ASN cc_start: 0.9225 (m-40) cc_final: 0.8528 (m110) REVERT: F 308 GLN cc_start: 0.9090 (pm20) cc_final: 0.8877 (pm20) REVERT: F 388 ILE cc_start: 0.9686 (mm) cc_final: 0.9459 (pt) REVERT: G 154 MET cc_start: 0.9482 (mpp) cc_final: 0.8894 (mpp) REVERT: S 1 MET cc_start: 0.7584 (ppp) cc_final: 0.7257 (ppp) REVERT: T 1 MET cc_start: 0.9487 (mpp) cc_final: 0.9230 (mmp) REVERT: T 48 PHE cc_start: 0.7520 (m-10) cc_final: 0.7117 (m-10) REVERT: M 59 GLU cc_start: 0.6314 (mp0) cc_final: 0.5855 (mp0) REVERT: Q 50 MET cc_start: 0.2830 (mmm) cc_final: 0.1999 (mmm) REVERT: X 81 ASN cc_start: 0.9461 (m-40) cc_final: 0.9109 (p0) REVERT: X 88 MET cc_start: 0.9314 (mmt) cc_final: 0.9099 (mmt) REVERT: X 135 TYR cc_start: 0.9344 (t80) cc_final: 0.8927 (t80) REVERT: X 220 MET cc_start: 0.9098 (ppp) cc_final: 0.8896 (ppp) REVERT: 6 90 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6762 (mm-30) REVERT: U 48 LEU cc_start: 0.9182 (mt) cc_final: 0.8875 (pt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.2068 time to fit residues: 173.6475 Evaluate side-chains 384 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 404 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 403 optimal weight: 7.9990 chunk 367 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 106 optimal weight: 0.3980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050506 restraints weight = 211768.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050428 restraints weight = 129433.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051560 restraints weight = 91233.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051412 restraints weight = 70024.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051524 restraints weight = 65162.144| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39409 Z= 0.170 Angle : 0.680 10.661 53398 Z= 0.346 Chirality : 0.046 0.395 6322 Planarity : 0.004 0.056 6814 Dihedral : 6.465 114.178 5556 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 5042 helix: 0.77 (0.10), residues: 2659 sheet: -0.57 (0.24), residues: 510 loop : -1.21 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 17 TYR 0.021 0.001 TYR X 247 PHE 0.041 0.002 PHE R 64 TRP 0.011 0.001 TRP 6 79 HIS 0.005 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00371 (39409) covalent geometry : angle 0.67977 (53398) hydrogen bonds : bond 0.04311 ( 2199) hydrogen bonds : angle 4.82135 ( 6375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.932 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: 8 27 PHE cc_start: 0.8339 (m-10) cc_final: 0.7936 (m-10) REVERT: Y 11 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8346 (mmm160) REVERT: Y 97 ARG cc_start: 0.8724 (tpm170) cc_final: 0.8155 (tpm170) REVERT: Y 98 LEU cc_start: 0.8922 (pp) cc_final: 0.8624 (pp) REVERT: Y 108 PHE cc_start: 0.9331 (t80) cc_final: 0.8957 (t80) REVERT: Y 112 ASN cc_start: 0.8158 (m110) cc_final: 0.7616 (m110) REVERT: Y 139 LYS cc_start: 0.9370 (mttp) cc_final: 0.9039 (mppt) REVERT: A 67 ASN cc_start: 0.8334 (t0) cc_final: 0.8010 (t0) REVERT: A 183 ASP cc_start: 0.8933 (m-30) cc_final: 0.8702 (m-30) REVERT: A 270 TYR cc_start: 0.9372 (m-80) cc_final: 0.9109 (m-10) REVERT: A 351 GLN cc_start: 0.9473 (pm20) cc_final: 0.9222 (pm20) REVERT: A 357 GLU cc_start: 0.9287 (tp30) cc_final: 0.9024 (tp30) REVERT: B 56 GLU cc_start: 0.8702 (mp0) cc_final: 0.8445 (mp0) REVERT: B 183 ASP cc_start: 0.9233 (m-30) cc_final: 0.8853 (m-30) REVERT: B 208 VAL cc_start: 0.9522 (m) cc_final: 0.9279 (m) REVERT: B 226 ASP cc_start: 0.9080 (t0) cc_final: 0.8582 (t0) REVERT: B 228 MET cc_start: 0.8785 (ppp) cc_final: 0.8247 (tpp) REVERT: B 275 LYS cc_start: 0.9626 (mtmt) cc_final: 0.9040 (mtpt) REVERT: B 361 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9380 (mmmt) REVERT: B 371 LEU cc_start: 0.9744 (mt) cc_final: 0.9220 (tt) REVERT: B 378 SER cc_start: 0.8882 (t) cc_final: 0.8607 (p) REVERT: B 399 TYR cc_start: 0.8913 (m-80) cc_final: 0.8645 (m-80) REVERT: B 470 PHE cc_start: 0.9514 (t80) cc_final: 0.9244 (t80) REVERT: C 270 TYR cc_start: 0.8981 (m-10) cc_final: 0.8560 (m-10) REVERT: D 197 LEU cc_start: 0.9799 (tt) cc_final: 0.9593 (tp) REVERT: D 201 MET cc_start: 0.9492 (mmp) cc_final: 0.8947 (mmm) REVERT: D 237 LEU cc_start: 0.9780 (tp) cc_final: 0.9503 (tp) REVERT: D 257 ASN cc_start: 0.9236 (t0) cc_final: 0.8613 (t0) REVERT: D 271 LEU cc_start: 0.9551 (mt) cc_final: 0.9225 (mt) REVERT: D 311 TYR cc_start: 0.9149 (t80) cc_final: 0.8936 (t80) REVERT: D 393 MET cc_start: 0.9221 (tpt) cc_final: 0.8882 (tpp) REVERT: D 459 MET cc_start: 0.9080 (mmp) cc_final: 0.8452 (mmm) REVERT: E 257 ASN cc_start: 0.9233 (t0) cc_final: 0.8647 (t0) REVERT: E 288 ASP cc_start: 0.9251 (m-30) cc_final: 0.8996 (m-30) REVERT: F 64 MET cc_start: 0.9084 (mmp) cc_final: 0.8564 (mmp) REVERT: F 97 ASN cc_start: 0.8775 (m110) cc_final: 0.8370 (m110) REVERT: F 257 ASN cc_start: 0.9237 (m-40) cc_final: 0.8509 (m110) REVERT: F 308 GLN cc_start: 0.9005 (pm20) cc_final: 0.8784 (pm20) REVERT: F 388 ILE cc_start: 0.9685 (mm) cc_final: 0.9463 (pt) REVERT: G 116 MET cc_start: 0.9451 (mpp) cc_final: 0.9158 (mpp) REVERT: G 154 MET cc_start: 0.9502 (mpp) cc_final: 0.8919 (mpp) REVERT: G 212 TYR cc_start: 0.7785 (t80) cc_final: 0.7464 (t80) REVERT: S 1 MET cc_start: 0.7616 (ppp) cc_final: 0.7303 (ppp) REVERT: T 1 MET cc_start: 0.9474 (mpp) cc_final: 0.9248 (mmp) REVERT: K 24 ILE cc_start: 0.7523 (tp) cc_final: 0.7131 (tp) REVERT: M 50 MET cc_start: 0.2605 (mpp) cc_final: 0.2359 (mpp) REVERT: X 81 ASN cc_start: 0.9442 (m-40) cc_final: 0.9116 (p0) REVERT: X 88 MET cc_start: 0.9318 (mmt) cc_final: 0.9010 (mmm) REVERT: X 135 TYR cc_start: 0.9322 (t80) cc_final: 0.8911 (t80) REVERT: X 220 MET cc_start: 0.9140 (ppp) cc_final: 0.8934 (ppp) REVERT: 6 90 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6612 (mm-30) REVERT: U 48 LEU cc_start: 0.9163 (mt) cc_final: 0.8837 (pp) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1985 time to fit residues: 168.6974 Evaluate side-chains 382 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 323 optimal weight: 50.0000 chunk 472 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 382 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.075614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050379 restraints weight = 213840.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050072 restraints weight = 130173.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050721 restraints weight = 98569.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051207 restraints weight = 71684.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051253 restraints weight = 64924.909| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39409 Z= 0.180 Angle : 0.691 10.445 53398 Z= 0.352 Chirality : 0.046 0.395 6322 Planarity : 0.004 0.049 6814 Dihedral : 6.453 114.135 5556 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.12), residues: 5042 helix: 0.71 (0.10), residues: 2716 sheet: -0.58 (0.24), residues: 512 loop : -1.28 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 40 TYR 0.021 0.001 TYR X 241 PHE 0.038 0.002 PHE B 395 TRP 0.012 0.001 TRP 6 79 HIS 0.011 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00394 (39409) covalent geometry : angle 0.69111 (53398) hydrogen bonds : bond 0.04327 ( 2199) hydrogen bonds : angle 4.84220 ( 6375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.128 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: 8 20 MET cc_start: 0.6167 (tmm) cc_final: 0.5845 (tmm) REVERT: 8 27 PHE cc_start: 0.8296 (m-10) cc_final: 0.7923 (m-10) REVERT: Y 84 TYR cc_start: 0.8540 (m-80) cc_final: 0.8153 (m-80) REVERT: Y 97 ARG cc_start: 0.8752 (tpm170) cc_final: 0.8151 (tpm170) REVERT: Y 98 LEU cc_start: 0.8904 (pp) cc_final: 0.8618 (pp) REVERT: Y 108 PHE cc_start: 0.9339 (t80) cc_final: 0.8975 (t80) REVERT: Y 112 ASN cc_start: 0.8026 (m110) cc_final: 0.7519 (m110) REVERT: A 67 ASN cc_start: 0.8342 (t0) cc_final: 0.8045 (t0) REVERT: A 183 ASP cc_start: 0.8934 (m-30) cc_final: 0.8683 (m-30) REVERT: A 270 TYR cc_start: 0.9373 (m-80) cc_final: 0.9116 (m-10) REVERT: A 351 GLN cc_start: 0.9469 (pm20) cc_final: 0.9209 (pm20) REVERT: A 357 GLU cc_start: 0.9279 (tp30) cc_final: 0.9026 (tp30) REVERT: B 183 ASP cc_start: 0.9246 (m-30) cc_final: 0.8853 (m-30) REVERT: B 226 ASP cc_start: 0.9156 (t0) cc_final: 0.8697 (t0) REVERT: B 228 MET cc_start: 0.8827 (ppp) cc_final: 0.8260 (tpp) REVERT: B 361 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9405 (mmmt) REVERT: B 371 LEU cc_start: 0.9746 (mt) cc_final: 0.9202 (tt) REVERT: B 378 SER cc_start: 0.8941 (t) cc_final: 0.8681 (p) REVERT: B 399 TYR cc_start: 0.8941 (m-80) cc_final: 0.8668 (m-80) REVERT: B 470 PHE cc_start: 0.9531 (t80) cc_final: 0.9165 (t80) REVERT: C 183 ASP cc_start: 0.8960 (m-30) cc_final: 0.8759 (m-30) REVERT: C 270 TYR cc_start: 0.8975 (m-10) cc_final: 0.8728 (m-10) REVERT: C 307 LEU cc_start: 0.9793 (tp) cc_final: 0.9500 (tp) REVERT: D 201 MET cc_start: 0.9492 (mmp) cc_final: 0.9213 (mmm) REVERT: D 237 LEU cc_start: 0.9777 (tp) cc_final: 0.9506 (tp) REVERT: D 257 ASN cc_start: 0.9246 (t0) cc_final: 0.8613 (t0) REVERT: D 271 LEU cc_start: 0.9560 (mt) cc_final: 0.9236 (mt) REVERT: D 311 TYR cc_start: 0.9152 (t80) cc_final: 0.8924 (t80) REVERT: D 393 MET cc_start: 0.9184 (tpt) cc_final: 0.8849 (tpp) REVERT: D 459 MET cc_start: 0.9056 (mmp) cc_final: 0.8612 (mmm) REVERT: E 74 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8379 (mt-10) REVERT: E 257 ASN cc_start: 0.9257 (t0) cc_final: 0.8658 (t0) REVERT: E 288 ASP cc_start: 0.9252 (m-30) cc_final: 0.8999 (m-30) REVERT: F 64 MET cc_start: 0.9136 (mmp) cc_final: 0.8568 (mmp) REVERT: F 97 ASN cc_start: 0.8765 (m110) cc_final: 0.8391 (m110) REVERT: F 201 MET cc_start: 0.9451 (mpp) cc_final: 0.8873 (mpp) REVERT: F 257 ASN cc_start: 0.9197 (m-40) cc_final: 0.8469 (m110) REVERT: F 308 GLN cc_start: 0.9054 (pm20) cc_final: 0.8845 (pm20) REVERT: F 388 ILE cc_start: 0.9681 (mm) cc_final: 0.9461 (pt) REVERT: G 154 MET cc_start: 0.9505 (mpp) cc_final: 0.8906 (mpp) REVERT: G 212 TYR cc_start: 0.7884 (t80) cc_final: 0.7579 (t80) REVERT: S 1 MET cc_start: 0.7676 (ppp) cc_final: 0.7360 (ppp) REVERT: T 1 MET cc_start: 0.9449 (mpp) cc_final: 0.9223 (mmp) REVERT: R 70 PHE cc_start: 0.8576 (m-80) cc_final: 0.8370 (m-80) REVERT: X 81 ASN cc_start: 0.9455 (m-40) cc_final: 0.9156 (p0) REVERT: X 88 MET cc_start: 0.9282 (mmt) cc_final: 0.8990 (mmt) REVERT: X 135 TYR cc_start: 0.9347 (t80) cc_final: 0.8940 (t80) REVERT: X 220 MET cc_start: 0.9157 (ppp) cc_final: 0.8819 (ppp) REVERT: 6 90 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6513 (mm-30) REVERT: U 48 LEU cc_start: 0.9151 (mt) cc_final: 0.8836 (pp) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2072 time to fit residues: 171.0482 Evaluate side-chains 380 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 13 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 483 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 434 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 55 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048725 restraints weight = 217384.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.048557 restraints weight = 132268.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049322 restraints weight = 100050.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049495 restraints weight = 74047.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.049569 restraints weight = 67460.663| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 39409 Z= 0.251 Angle : 0.747 9.691 53398 Z= 0.382 Chirality : 0.047 0.390 6322 Planarity : 0.005 0.073 6814 Dihedral : 6.576 115.831 5556 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 5042 helix: 0.60 (0.10), residues: 2732 sheet: -0.59 (0.23), residues: 519 loop : -1.35 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 17 TYR 0.018 0.002 TYR D 381 PHE 0.036 0.002 PHE Y 13 TRP 0.018 0.002 TRP 6 79 HIS 0.010 0.002 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00539 (39409) covalent geometry : angle 0.74712 (53398) hydrogen bonds : bond 0.04549 ( 2199) hydrogen bonds : angle 4.99485 ( 6375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.355 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: 8 20 MET cc_start: 0.6110 (tmm) cc_final: 0.5814 (tmm) REVERT: 8 27 PHE cc_start: 0.8101 (m-10) cc_final: 0.7712 (m-10) REVERT: Y 97 ARG cc_start: 0.8823 (tpm170) cc_final: 0.8210 (tpm170) REVERT: Y 98 LEU cc_start: 0.8921 (pp) cc_final: 0.8678 (pp) REVERT: Y 108 PHE cc_start: 0.9329 (t80) cc_final: 0.8960 (t80) REVERT: Y 112 ASN cc_start: 0.8006 (m110) cc_final: 0.7407 (m110) REVERT: Y 139 LYS cc_start: 0.9404 (mttp) cc_final: 0.9067 (mppt) REVERT: A 67 ASN cc_start: 0.8345 (t0) cc_final: 0.8012 (t0) REVERT: A 183 ASP cc_start: 0.8938 (m-30) cc_final: 0.8702 (m-30) REVERT: A 270 TYR cc_start: 0.9411 (m-80) cc_final: 0.9184 (m-10) REVERT: A 351 GLN cc_start: 0.9481 (pm20) cc_final: 0.9218 (pm20) REVERT: A 357 GLU cc_start: 0.9285 (tp30) cc_final: 0.9054 (tp30) REVERT: B 183 ASP cc_start: 0.9215 (m-30) cc_final: 0.8815 (m-30) REVERT: B 226 ASP cc_start: 0.9219 (t0) cc_final: 0.8793 (t0) REVERT: B 228 MET cc_start: 0.8806 (ppp) cc_final: 0.8158 (tpp) REVERT: B 275 LYS cc_start: 0.9579 (mtmt) cc_final: 0.9260 (mtmm) REVERT: B 361 LYS cc_start: 0.9597 (mmmt) cc_final: 0.9385 (mmmt) REVERT: B 371 LEU cc_start: 0.9766 (mt) cc_final: 0.9270 (tt) REVERT: B 378 SER cc_start: 0.8976 (t) cc_final: 0.8757 (p) REVERT: C 183 ASP cc_start: 0.8969 (m-30) cc_final: 0.8753 (m-30) REVERT: C 270 TYR cc_start: 0.8991 (m-10) cc_final: 0.8563 (m-10) REVERT: C 307 LEU cc_start: 0.9793 (tp) cc_final: 0.9554 (tp) REVERT: D 257 ASN cc_start: 0.9279 (t0) cc_final: 0.8647 (t0) REVERT: D 271 LEU cc_start: 0.9598 (mt) cc_final: 0.9276 (mt) REVERT: D 311 TYR cc_start: 0.9140 (t80) cc_final: 0.8915 (t80) REVERT: D 393 MET cc_start: 0.9188 (tpt) cc_final: 0.8834 (tpp) REVERT: D 459 MET cc_start: 0.9048 (mmp) cc_final: 0.8516 (mmm) REVERT: E 74 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8393 (mt-10) REVERT: E 257 ASN cc_start: 0.9327 (t0) cc_final: 0.8754 (t0) REVERT: E 289 MET cc_start: 0.9424 (ttp) cc_final: 0.9179 (tmm) REVERT: F 64 MET cc_start: 0.9152 (mmp) cc_final: 0.8601 (mmp) REVERT: F 97 ASN cc_start: 0.8769 (m110) cc_final: 0.8405 (m110) REVERT: F 201 MET cc_start: 0.9399 (mpp) cc_final: 0.8912 (mpp) REVERT: F 257 ASN cc_start: 0.9261 (m-40) cc_final: 0.8592 (m110) REVERT: F 388 ILE cc_start: 0.9706 (mm) cc_final: 0.9497 (pt) REVERT: G 116 MET cc_start: 0.9468 (mpp) cc_final: 0.9178 (mpp) REVERT: G 154 MET cc_start: 0.9554 (mpp) cc_final: 0.8940 (mpp) REVERT: G 175 PHE cc_start: 0.9109 (p90) cc_final: 0.8841 (p90) REVERT: G 212 TYR cc_start: 0.7981 (t80) cc_final: 0.7714 (t80) REVERT: S 1 MET cc_start: 0.7739 (ppp) cc_final: 0.7419 (ppp) REVERT: R 70 PHE cc_start: 0.8578 (m-80) cc_final: 0.8336 (m-80) REVERT: X 81 ASN cc_start: 0.9446 (m-40) cc_final: 0.9133 (p0) REVERT: X 88 MET cc_start: 0.9267 (mmt) cc_final: 0.9019 (mmt) REVERT: X 135 TYR cc_start: 0.9350 (t80) cc_final: 0.8949 (t80) REVERT: X 220 MET cc_start: 0.9180 (ppp) cc_final: 0.8878 (ppp) REVERT: 7 21 ILE cc_start: 0.7417 (tp) cc_final: 0.7122 (tp) REVERT: 6 9 ARG cc_start: 0.9379 (ttt-90) cc_final: 0.8744 (ttp-170) REVERT: 6 90 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6419 (mm-30) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.2102 time to fit residues: 170.6892 Evaluate side-chains 374 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 210 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 357 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 55 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.075467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049859 restraints weight = 212700.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049777 restraints weight = 127346.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051328 restraints weight = 91423.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051060 restraints weight = 61386.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051157 restraints weight = 59876.706| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 39409 Z= 0.149 Angle : 0.699 11.172 53398 Z= 0.354 Chirality : 0.046 0.390 6322 Planarity : 0.004 0.070 6814 Dihedral : 6.473 114.477 5556 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.55 % Favored : 94.27 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.12), residues: 5042 helix: 0.70 (0.10), residues: 2721 sheet: -0.47 (0.24), residues: 517 loop : -1.21 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 8 42 TYR 0.020 0.001 TYR X 241 PHE 0.042 0.002 PHE R 64 TRP 0.014 0.001 TRP B 191 HIS 0.011 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00327 (39409) covalent geometry : angle 0.69893 (53398) hydrogen bonds : bond 0.04322 ( 2199) hydrogen bonds : angle 4.83201 ( 6375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6500.01 seconds wall clock time: 113 minutes 41.30 seconds (6821.30 seconds total)