Starting phenix.real_space_refine on Fri Jun 27 08:12:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmq_25999/06_2025/7tmq_25999.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.147 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 2 5.49 5 Mg 1 5.21 5 S 90 5.16 5 C 20279 2.51 5 N 5709 2.21 5 O 5561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31642 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4241 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 560} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 28, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3424 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 20, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4043 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 519 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 31, 'PHE:plan': 3, 'GLU:plan': 33, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 334 Chain: "D" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3320 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 25, 'ASN:plan1': 8, 'ARG:plan': 1, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 207 Chain: "E" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4117 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 553} Chain breaks: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 24, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 245 Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3300 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 26, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1063 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 16, 'ASN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 299 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1360 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "J" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 581 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "K" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1322 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 200 Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 486 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1286 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 284 Chain: "N" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 561 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 196 Chain: "P" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2211 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 1399 Unresolved non-hydrogen angles: 1785 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" 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: 18.59, per 1000 atoms: 0.59 Number of scatterers: 31642 At special positions: 0 Unit cell: (147.29, 136.99, 201.88, 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 90 16.00 P 2 15.00 Mg 1 11.99 O 5561 8.00 N 5709 7.00 C 20279 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: 9.15 Conformation dependent library (CDL) restraints added in 4.8 seconds 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8840 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 42 sheets defined 53.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.611A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.664A pdb=" N MET A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.628A pdb=" N GLY A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 307 " --> pdb=" O MET A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 307' Processing helix chain 'A' and resid 327 through 347 removed outlier: 4.124A pdb=" N ALA A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.760A pdb=" N ASP A 422 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 477 through 503 removed outlier: 4.098A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 614 removed outlier: 3.657A pdb=" N ARG A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.568A pdb=" N GLN B 18 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.567A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.654A pdb=" N THR B 238 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.127A pdb=" N ARG B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 325 through 345 removed outlier: 4.806A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 463 through 474 removed outlier: 4.569A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 502 Processing helix chain 'C' and resid 503 through 507 Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 587 removed outlier: 3.700A pdb=" N SER C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 613 removed outlier: 3.971A pdb=" N GLU C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.955A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 248 through 271 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 307 through 318 Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 395 through 421 removed outlier: 4.143A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 325 through 346 removed outlier: 4.389A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 426 through 435 Processing helix chain 'E' and resid 442 through 448 Processing helix chain 'E' and resid 463 through 475 removed outlier: 4.768A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 563 Processing helix chain 'E' and resid 566 through 574 Processing helix chain 'E' and resid 574 through 584 Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 611 removed outlier: 3.788A pdb=" N GLN E 608 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.616A pdb=" N LEU F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 232 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 306 No H-bonds generated for 'chain 'F' and resid 305 through 306' Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 368 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 425 removed outlier: 7.137A pdb=" N GLU F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLU F 423 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 425 " --> pdb=" O GLY F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'G' and resid 76 through 114 removed outlier: 3.946A pdb=" N GLY G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 133 removed outlier: 3.684A pdb=" N ILE G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 164 removed outlier: 5.446A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'H' and resid 64 through 104 removed outlier: 5.145A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 114 removed outlier: 3.600A pdb=" N THR I 48 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 removed outlier: 3.600A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 202 through 214 Processing helix chain 'I' and resid 214 through 223 Processing helix chain 'J' and resid 6 through 63 Processing helix chain 'J' and resid 64 through 104 removed outlier: 3.543A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 113 removed outlier: 3.577A pdb=" N ASN K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix removed outlier: 3.531A pdb=" N ALA K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 164 removed outlier: 5.567A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 214 through 224 Processing helix chain 'L' and resid 26 through 63 Processing helix chain 'L' and resid 67 through 91 removed outlier: 4.028A pdb=" N LYS L 71 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 104 removed outlier: 4.220A pdb=" N LYS L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 76 Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 115 through 118 removed outlier: 3.620A pdb=" N ASN M 118 " --> pdb=" O PRO M 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 115 through 118' Processing helix chain 'M' and resid 128 through 176 Processing helix chain 'M' and resid 176 through 217 Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.767A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 106 through 112 Processing helix chain 'P' and resid 10 through 23 removed outlier: 3.725A pdb=" N ARG P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 33 Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 76 through 87 Processing helix chain 'P' and resid 89 through 106 Processing helix chain 'P' and resid 110 through 120 Processing helix chain 'P' and resid 120 through 131 Processing helix chain 'P' and resid 135 through 152 removed outlier: 4.130A pdb=" N GLN P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 167 Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 179 through 194 Processing helix chain 'P' and resid 196 through 210 Processing helix chain 'P' and resid 210 through 223 removed outlier: 3.582A pdb=" N LEU P 214 " --> pdb=" O PHE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 256 removed outlier: 4.176A pdb=" N ASN P 256 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 removed outlier: 3.527A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR P 267 " --> pdb=" O LEU P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 281 Processing helix chain 'P' and resid 283 through 298 Processing helix chain 'P' and resid 304 through 316 Processing helix chain 'P' and resid 317 through 328 Processing helix chain 'P' and resid 332 through 353 removed outlier: 3.736A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 Processing helix chain 'P' and resid 371 through 376 Processing helix chain 'P' and resid 376 through 408 removed outlier: 4.986A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 411 No H-bonds generated for 'chain 'P' and resid 409 through 411' Processing helix chain 'P' and resid 413 through 433 Processing helix chain 'P' and resid 435 through 444 removed outlier: 4.116A pdb=" N ASP P 439 " --> pdb=" O PRO P 435 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 455 removed outlier: 3.783A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 458 through 473 Processing sheet with id=AA1, first strand: chain 'I' and resid 171 through 174 removed outlier: 4.017A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE F 40 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 69 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 63 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A 27 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 48 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 5.486A pdb=" N TYR A 105 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A 321 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 350 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER A 409 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET A 352 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS A 397 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.764A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 5.719A pdb=" N ILE A 182 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU A 201 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414 removed outlier: 6.268A pdb=" N THR A 252 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.973A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE K 197 " --> pdb=" O ASN K 192 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU C 48 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 47 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB1, first strand: chain 'B' and resid 112 through 114 removed outlier: 6.342A pdb=" N VAL B 274 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.340A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.049A pdb=" N ILE B 172 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN B 357 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU B 376 " --> pdb=" O GLN B 357 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 359 " --> pdb=" O ASN B 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=AB5, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.754A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 410 " --> pdb=" O GLY C 396 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.754A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 414 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.853A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.693A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 185 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE C 197 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 207 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 232 through 233 removed outlier: 4.574A pdb=" N CYS C 246 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 removed outlier: 3.646A pdb=" N GLU C 309 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 377 removed outlier: 6.290A pdb=" N PHE C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 171 through 174 removed outlier: 6.079A pdb=" N ILE G 197 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 86 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU E 48 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU E 47 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AC5, first strand: chain 'D' and resid 111 through 113 removed outlier: 3.761A pdb=" N ARG D 111 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 212 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR D 279 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.148A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC8, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.593A pdb=" N PHE D 173 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N GLN D 357 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU D 376 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE D 359 " --> pdb=" O ASN D 374 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AD1, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.893A pdb=" N ILE E 278 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL E 318 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR E 280 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN E 320 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY E 282 " --> pdb=" O ASN E 320 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 277 " --> pdb=" O ASN E 349 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 170 through 173 removed outlier: 3.962A pdb=" N GLY E 159 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AD4, first strand: chain 'E' and resid 232 through 233 removed outlier: 4.465A pdb=" N CYS E 246 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD6, first strand: chain 'E' and resid 375 through 377 removed outlier: 6.171A pdb=" N PHE E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 437 through 441 removed outlier: 10.124A pdb=" N PHE E 438 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER E 457 " --> pdb=" O PHE E 438 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY E 440 " --> pdb=" O ASN E 455 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 101 through 104 Processing sheet with id=AD9, first strand: chain 'F' and resid 112 through 113 Processing sheet with id=AE1, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.117A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 329 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL F 274 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 164 through 165 removed outlier: 4.502A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 192 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.514A pdb=" N PHE F 173 " --> pdb=" O VAL F 360 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 92 through 97 Processing sheet with id=AE5, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.366A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN N 70 " --> pdb=" O ALA N 9 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 28 through 29 2179 hydrogen bonds defined for protein. 6309 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: 13.80 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5160 1.30 - 1.43: 7748 1.43 - 1.55: 19112 1.55 - 1.68: 4 1.68 - 1.81: 163 Bond restraints: 32187 Sorted by residual: bond pdb=" CA TYR D 265 " pdb=" C TYR D 265 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.34e-02 5.57e+03 5.84e+01 bond pdb=" CA GLU A 47 " pdb=" C GLU A 47 " ideal model delta sigma weight residual 1.528 1.430 0.098 1.35e-02 5.49e+03 5.28e+01 bond pdb=" CA THR F 354 " pdb=" C THR F 354 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.34e-02 5.57e+03 3.90e+01 bond pdb=" CA ALA B 165 " pdb=" C ALA B 165 " ideal model delta sigma weight residual 1.527 1.445 0.082 1.41e-02 5.03e+03 3.35e+01 bond pdb=" CA THR D 350 " pdb=" C THR D 350 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.30e-02 5.92e+03 3.00e+01 ... (remaining 32182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 43775 2.69 - 5.39: 299 5.39 - 8.08: 29 8.08 - 10.78: 2 10.78 - 13.47: 2 Bond angle restraints: 44107 Sorted by residual: angle pdb=" N GLU D 129 " pdb=" CA GLU D 129 " pdb=" C GLU D 129 " ideal model delta sigma weight residual 113.88 100.41 13.47 1.23e+00 6.61e-01 1.20e+02 angle pdb=" N ARG B 166 " pdb=" CA ARG B 166 " pdb=" C ARG B 166 " ideal model delta sigma weight residual 111.28 121.93 -10.65 1.09e+00 8.42e-01 9.55e+01 angle pdb=" N ASN C 288 " pdb=" CA ASN C 288 " pdb=" C ASN C 288 " ideal model delta sigma weight residual 111.28 104.92 6.36 1.09e+00 8.42e-01 3.41e+01 angle pdb=" N VAL L 95 " pdb=" CA VAL L 95 " pdb=" C VAL L 95 " ideal model delta sigma weight residual 109.34 98.48 10.86 2.08e+00 2.31e-01 2.73e+01 angle pdb=" N THR D 354 " pdb=" CA THR D 354 " pdb=" C THR D 354 " ideal model delta sigma weight residual 110.19 116.47 -6.28 1.24e+00 6.50e-01 2.56e+01 ... (remaining 44102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 18848 34.38 - 68.75: 250 68.75 - 103.13: 27 103.13 - 137.50: 0 137.50 - 171.88: 2 Dihedral angle restraints: 19127 sinusoidal: 5431 harmonic: 13696 Sorted by residual: dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 111.88 -171.88 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP A 702 " pdb=" O5' ADP A 702 " pdb=" PA ADP A 702 " pdb=" O2A ADP A 702 " ideal model delta sinusoidal sigma weight residual 300.00 130.37 169.64 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA THR E 315 " pdb=" C THR E 315 " pdb=" N THR E 316 " pdb=" CA THR E 316 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 19124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5063 0.086 - 0.172: 368 0.172 - 0.257: 8 0.257 - 0.343: 1 0.343 - 0.429: 2 Chirality restraints: 5442 Sorted by residual: chirality pdb=" CA ARG B 166 " pdb=" N ARG B 166 " pdb=" C ARG B 166 " pdb=" CB ARG B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE I 172 " pdb=" CA ILE I 172 " pdb=" CG1 ILE I 172 " pdb=" CG2 ILE I 172 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE C 167 " pdb=" CA ILE C 167 " pdb=" CG1 ILE C 167 " pdb=" CG2 ILE C 167 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5439 not shown) Planarity restraints: 5734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 417 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO C 418 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 418 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 418 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 348 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASP F 348 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP F 348 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU F 349 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 286 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ARG C 286 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 286 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 287 " 0.012 2.00e-02 2.50e+03 ... (remaining 5731 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 218 2.60 - 3.18: 27704 3.18 - 3.75: 52244 3.75 - 4.33: 67571 4.33 - 4.90: 116774 Nonbonded interactions: 264511 Sorted by model distance: nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 701 " model vdw 2.026 2.170 nonbonded pdb="MG MG A 701 " pdb=" O1B ADP A 702 " model vdw 2.072 2.170 nonbonded pdb=" O ASN E 39 " pdb=" ND2 ASN E 39 " model vdw 2.110 3.120 nonbonded pdb=" OE1 GLU B 129 " pdb=" OH TYR B 265 " model vdw 2.197 3.040 nonbonded pdb=" O ILE F 52 " pdb=" OG1 THR F 96 " model vdw 2.218 3.040 ... (remaining 264506 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 24 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 65 or (resid 66 and (name N or nam \ e CA or name C or name O or name CB )) or resid 67 through 73 or (resid 74 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or r \ esid 84 through 101 or (resid 102 and (name N or name CA or name C or name O or \ name CB )) or resid 103 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 116 or (resid 117 th \ rough 121 and (name N or name CA or name C or name O or name CB )) or resid 122 \ through 129 or (resid 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 through 146 or (resid 147 through 148 and (name N or name CA or \ name C or name O or name CB )) or resid 149 or (resid 150 and (name N or name CA \ or name C or name O or name CB )) or resid 151 through 155 or (resid 156 and (n \ ame N or name CA or name C or name O or name CB )) or resid 157 through 176 or ( \ resid 177 through 178 and (name N or name CA or name C or name O or name CB )) o \ r resid 179 through 180 or (resid 181 and (name N or name CA or name C or name O \ or name CB )) or resid 182 or (resid 183 and (name N or name CA or name C or na \ me O or name CB )) or resid 184 through 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 198 or (resid 199 and (name N or name CA or name C or name O or name CB )) o \ r resid 200 through 205 or (resid 206 through 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 223 or (resid 224 through 225 an \ d (name N or name CA or name C or name O or name CB )) or resid 226 through 234 \ or (resid 235 and (name N or name CA or name C or name O or name CB )) or resid \ 236 through 240 or (resid 241 through 242 and (name N or name CA or name C or na \ me O or name CB )) or resid 243 through 257 or (resid 258 and (name N or name CA \ or name C or name O or name CB )) or resid 259 or (resid 260 and (name N or nam \ e CA or name C or name O or name CB )) or resid 261 or (resid 262 through 271 an \ d (name N or name CA or name C or name O or name CB )) or resid 272 or (resid 27 \ 3 through 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 288 or (resid 289 and (name N or name CA or name C or name O or name \ CB )) or resid 290 through 294 or (resid 295 through 296 and (name N or name CA \ or name C or name O or name CB )) or resid 297 through 301 or (resid 302 throug \ h 305 and (name N or name CA or name C or name O or name CB )) or (resid 306 thr \ ough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 o \ r (resid 311 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 12 through 314 or (resid 315 and (name N or name CA or name C or name O or name \ CB )) or resid 316 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 354 or (resid 355 through 358 and (na \ me N or name CA or name C or name O or name CB )) or resid 359 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 367 or (resid 368 and (name N or name CA or name C or name O \ or name CB )) or resid 369 through 377 or (resid 378 and (name N or name CA or n \ ame C or name O or name CB )) or resid 379 through 389 or (resid 390 and (name N \ or name CA or name C or name O or name CB )) or resid 391 through 417 or resid \ 425 through 442 or (resid 443 through 444 and (name N or name CA or name C or na \ me O or name CB )) or resid 445 through 446 or (resid 447 through 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 452 or (resi \ d 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or ( \ resid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 \ through 457 or (resid 458 through 459 and (name N or name CA or name C or name O \ or name CB )) or resid 460 through 464 or (resid 465 and (name N or name CA or \ name C or name O or name CB )) or resid 466 through 467 or (resid 468 through 46 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 470 through \ 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) or re \ sid 475 through 483 or (resid 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 through 490 or (resid 491 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 512 and (name N or \ name CA or name C or name O or name CB )) or resid 513 through 514 or (resid 515 \ through 516 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 17 through 528 or (resid 529 and (name N or name CA or name C or name O or name \ CB )) or resid 530 or (resid 531 through 533 and (name N or name CA or name C or \ name O or name CB )) or resid 534 through 537 or (resid 538 and (name N or name \ CA or name C or name O or name CB )) or resid 539 through 544 or (resid 545 and \ (name N or name CA or name C or name O or name CB )) or resid 546 through 557 o \ r (resid 558 through 563 and (name N or name CA or name C or name O or name CB ) \ ) or resid 564 through 569 or (resid 570 through 574 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 575 through 580 and (name N or name CA o \ r name C or name O or name CB )) or resid 581 through 583 or (resid 584 through \ 585 and (name N or name CA or name C or name O or name CB )) or resid 586 throug \ h 587 or (resid 588 and (name N or name CA or name C or name O or name CB )) or \ resid 589 through 590 or (resid 591 and (name N or name CA or name C or name O o \ r name CB )) or resid 592 through 602 or (resid 603 through 613 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 35 or (resid 36 through 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thr \ ough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 73 or (resid 74 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 through 82 or (resid 83 and (name N or name CA \ or name C or name O or name CB )) or resid 84 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 107 or (resi \ d 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thro \ ugh 118 or (resid 119 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 through 129 or (resid 130 and (name N or name CA or name \ C or name O or name CB )) or resid 131 through 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 159 or (resid 16 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 176 or (resid 177 through 178 and (name N or name CA or name C or name O or name \ CB )) or resid 179 through 180 or (resid 181 and (name N or name CA or name C o \ r name O or name CB )) or resid 182 or (resid 183 and (name N or name CA or name \ C or name O or name CB )) or resid 184 through 194 or (resid 195 through 196 an \ d (name N or name CA or name C or name O or name CB )) or resid 197 through 204 \ or (resid 205 through 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 223 or (resid 224 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 through 234 or (resid 235 and (name \ N or name CA or name C or name O or name CB )) or resid 236 through 250 or (resi \ d 251 and (name N or name CA or name C or name O or name CB )) or resid 252 thro \ ugh 261 or (resid 262 through 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 273 or (resid 274 through 277 and (name N or nam \ e CA or name C or name O or name CB )) or resid 278 through 291 or (resid 292 an \ d (name N or name CA or name C or name O or name CB )) or resid 293 through 321 \ or (resid 322 and (name N or name CA or name C or name O or name CB )) or resid \ 323 through 410 or (resid 411 and (name N or name CA or name C or name O or name \ CB )) or resid 412 through 415 or (resid 416 through 417 and (name N or name CA \ or name C or name O or name CB )) or resid 425 through 452 or (resid 453 and (n \ ame N or name CA or name C or name O or name CB )) or resid 454 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 537 or (resid 538 and (name N or name CA or name C or name O \ or name CB )) or resid 539 through 613)) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 through 35 or (resid 36 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or \ name CA or name C or name O or name CB )) or resid 42 or (resid 43 through 44 an \ d (name N or name CA or name C or name O or name CB )) or resid 45 through 50 or \ (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 \ through 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 through 58 or (resid 59 and (name N or name CA or name C or name O \ or name CB )) or resid 60 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 133 or (resid 134 \ and (name N or name CA or name C or name O or name CB )) or resid 135 through 2 \ 05 or (resid 206 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 250 or (resid 251 and (name N or name CA or name C or \ name O or name CB )) or resid 252 through 275 or (resid 276 through 277 and (na \ me N or name CA or name C or name O or name CB )) or resid 278 through 284 or (r \ esid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 t \ hrough 288 or (resid 289 and (name N or name CA or name C or name O or name CB ) \ ) or resid 290 through 301 or (resid 302 through 305 and (name N or name CA or n \ ame C or name O or name CB )) or resid 306 through 310 or (resid 311 and (name N \ or name CA or name C or name O or name CB )) or resid 312 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 329 or (resid 330 through 332 and (name N or name CA or name \ C or name O or name CB )) or resid 333 through 350 or (resid 351 and (name N or \ name CA or name C or name O or name CB )) or resid 352 through 356 or (resid 357 \ through 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 361 or (resid 362 through 363 and (name N or name CA or name C or nam \ e O or name CB )) or resid 364 through 365 or (resid 366 and (name N or name CA \ or name C or name O or name CB )) or resid 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 377 or (resid 378 and \ (name N or name CA or name C or name O or name CB )) or resid 379 through 404 o \ r (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 06 or (resid 407 and (name N or name CA or name C or name O or name CB )) or res \ id 408 through 415 or (resid 416 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 through 446 or (resid 447 through 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 through 454 or (r \ esid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 t \ hrough 458 or (resid 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 467 or (resid 468 through 469 and (name N or name CA or n \ ame C or name O or name CB )) or resid 470 through 482 or (resid 483 through 484 \ and (name N or name CA or name C or name O or name CB )) or resid 485 through 4 \ 90 or (resid 491 through 502 and (name N or name CA or name C or name O or name \ CB )) or (resid 503 through 512 and (name N or name CA or name C or name O or na \ me CB )) or resid 513 through 514 or (resid 515 through 516 and (name N or name \ CA or name C or name O or name CB )) or resid 517 through 530 or (resid 531 thro \ ugh 533 and (name N or name CA or name C or name O or name CB )) or resid 534 th \ rough 557 or (resid 558 through 563 and (name N or name CA or name C or name O o \ r name CB )) or resid 564 through 569 or (resid 570 through 574 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 575 through 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 or (resid 582 through 5 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 586 through \ 589 or (resid 590 through 591 and (name N or name CA or name C or name O or nam \ e CB )) or resid 592 through 602 or (resid 603 through 613 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 17 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 98 or (resid 99 and ( \ name N or name CA or name C or name O or name CB )) or resid 100 through 105 or \ (resid 106 through 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 120 or (resid 121 through 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 136 or (resid 137 and (name N o \ r name CA or name C or name O or name CB )) or resid 138 through 147 or (resid 1 \ 48 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 through 151 or (resid 152 and (name N or name CA or name C or name O or nam \ e CB )) or resid 153 through 155 or (resid 156 through 157 and (name N or name C \ A or name C or name O or name CB )) or resid 158 through 161 or (resid 162 throu \ gh 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thr \ ough 194 or (resid 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 or (resid 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB )) or resid 219 through 220 or (resid 221 through 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 225 or (res \ id 226 through 228 and (name N or name CA or name C or name O or name CB )) or r \ esid 229 or (resid 230 through 232 and (name N or name CA or name C or name O or \ name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 237 or (resid 238 through 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 245 or (resid 2 \ 46 through 247 and (name N or name CA or name C or name O or name CB )) or resid \ 248 through 250 or (resid 251 and (name N or name CA or name C or name O or nam \ e CB )) or resid 252 through 263 or (resid 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 270 or (resid 271 and (name N or na \ me CA or name C or name O or name CB )) or resid 272 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB )) or resid 284 through 285 \ or (resid 286 through 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 312 or (resid 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 316 or \ (resid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 \ through 325 or (resid 326 and (name N or name CA or name C or name O or name CB \ )) or resid 327 through 333 or (resid 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 340 or (resid 341 and (name N or name C \ A or name C or name O or name CB )) or resid 342 or (resid 343 and (name N or na \ me CA or name C or name O or name CB )) or resid 344 through 377 or (resid 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 through \ 383 or (resid 384 through 387 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 388 through 392 and (name N or name CA or name C or name O or \ name CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name \ C or name O or name CB )) or resid 396 through 399 or (resid 400 through 401 an \ d (name N or name CA or name C or name O or name CB )) or resid 402 through 415 \ or (resid 416 through 420 and (name N or name CA or name C or name O or name CB \ )) or (resid 421 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or name C or \ name O or name CB )) or resid 439 through 440 or (resid 441 through 442 and (na \ me N or name CA or name C or name O or name CB )) or resid 443 through 455 or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 t \ hrough 458 or (resid 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 469 or (resid 470 through 472 and (name N or name CA or n \ ame C or name O or name CB )) or resid 473 or (resid 474 and (name N or name CA \ or name C or name O or name CB )) or resid 475 through 476 or (resid 477 and (na \ me N or name CA or name C or name O or name CB )) or resid 478 through 485)) selection = (chain 'D' and (resid 17 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 50 or (resid 51 throu \ gh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or r \ esid 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or \ resid 74 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB )) or resid 126 through 148 or (resid 149 and (name N \ or name CA or name C or name O or name CB )) or resid 150 through 151 or (resid \ 152 and (name N or name CA or name C or name O or name CB )) or resid 153 throug \ h 155 or (resid 156 through 157 and (name N or name CA or name C or name O or na \ me CB )) or resid 158 through 161 or (resid 162 through 163 and (name N or name \ CA or name C or name O or name CB )) or resid 164 through 220 or (resid 221 thro \ ugh 222 and (name N or name CA or name C or name O or name CB )) or resid 223 th \ rough 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) \ or resid 233 through 237 or (resid 238 through 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 245 or (resid 246 through 247 \ and (name N or name CA or name C or name O or name CB )) or resid 248 through 26 \ 3 or (resid 264 and (name N or name CA or name C or name O or name CB )) or resi \ d 265 through 316 or (resid 317 and (name N or name CA or name C or name O or na \ me CB )) or resid 318 through 384 or (resid 385 through 387 and (name N or name \ CA or name C or name O or name CB )) or (resid 388 through 392 and (name N or na \ me CA or name C or name O or name CB )) or resid 393 or (resid 394 through 395 a \ nd (name N or name CA or name C or name O or name CB )) or resid 396 through 415 \ or (resid 416 through 420 and (name N or name CA or name C or name O or name CB \ )) or (resid 421 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or name C o \ r name O or name CB )) or resid 439 through 440 or (resid 441 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or resid 443 through 455 or ( \ resid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ through 482 or (resid 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 485)) selection = (chain 'F' and ((resid 17 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 42 or (resid 43 and (name N or na \ me CA or name C or name O or name CB )) or resid 44 through 50 or (resid 51 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or \ resid 62 through 117 or (resid 118 and (name N or name CA or name C or name O or \ name CB )) or resid 119 through 120 or (resid 121 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 208 or (resid 209 a \ nd (name N or name CA or name C or name O or name CB )) or resid 210 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 225 or (resid 226 through 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 289 or (resid 290 and ( \ name N or name CA or name C or name O or name CB )) or resid 291 through 296 or \ (resid 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ through 322 or (resid 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 through 333 or (resid 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 338 or (resid 339 through 341 and (name \ N or name CA or name C or name O or name CB )) or resid 342 through 347 or (res \ id 348 and (name N or name CA or name C or name O or name CB )) or resid 349 thr \ ough 391 or (resid 392 and (name N or name CA or name C or name O or name CB )) \ or resid 393 through 400 or (resid 401 and (name N or name CA or name C or name \ O or name CB )) or resid 402 through 458 or (resid 459 and (name N or name CA or \ name C or name O or name CB )) or resid 460 through 469 or (resid 470 through 4 \ 72 and (name N or name CA or name C or name O or name CB )) or resid 473 or (res \ id 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thr \ ough 485)) } ncs_group { reference = (chain 'I' and (resid 27 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 102 or (resid 103 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thr \ ough 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) \ or resid 124 through 133 or (resid 134 and (name N or name CA or name C or name \ O or name CB )) or resid 135 through 183 or (resid 184 through 185 and (name N o \ r name CA or name C or name O or name CB )) or resid 186 through 193 or (resid 1 \ 94 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 210 or (resid 211 through 214 and (name N or name CA or name C or n \ ame O or name CB )) or resid 215 through 227 or (resid 228 and (name N or name C \ A or name C or name O or name CB )) or resid 229 or (resid 230 and (name N or na \ me CA or name C or name O or name CB )) or resid 231)) selection = (chain 'K' and (resid 27 through 77 or (resid 78 through 85 and (name N or name \ CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N or nam \ e CA or name C or name O or name CB )) or resid 88 through 94 or (resid 95 and ( \ name N or name CA or name C or name O or name CB )) or resid 96 through 105 or ( \ resid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ through 109 or (resid 110 through 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 126 or (resid 127 through 128 and (name N or \ name CA or name C or name O or name CB )) or resid 129 through 164 or (resid 16 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 166 through \ 231)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 75.010 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 32187 Z= 0.245 Angle : 0.573 13.475 44107 Z= 0.321 Chirality : 0.043 0.429 5442 Planarity : 0.004 0.055 5734 Dihedral : 12.666 171.880 10287 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 0.38 % Allowed : 0.43 % Favored : 99.19 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4694 helix: 2.30 (0.11), residues: 2343 sheet: -1.64 (0.22), residues: 548 loop : -0.23 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.004 0.001 HIS B 180 PHE 0.013 0.001 PHE F 439 TYR 0.014 0.001 TYR B 49 ARG 0.008 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.15630 ( 2167) hydrogen bonds : angle 6.41920 ( 6309) covalent geometry : bond 0.00422 (32187) covalent geometry : angle 0.57320 (44107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 416 time to evaluate : 3.490 Fit side-chains REVERT: B 166 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6907 (mtt-85) REVERT: C 39 ASN cc_start: 0.8123 (t0) cc_final: 0.7519 (t0) REVERT: C 224 THR cc_start: 0.8668 (p) cc_final: 0.8436 (p) REVERT: D 161 MET cc_start: 0.8426 (mtp) cc_final: 0.8213 (mtp) REVERT: D 355 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: E 134 ASP cc_start: 0.7770 (p0) cc_final: 0.7411 (p0) REVERT: E 302 THR cc_start: 0.7769 (m) cc_final: 0.7156 (p) REVERT: K 200 ASN cc_start: 0.8921 (t0) cc_final: 0.8473 (t0) outliers start: 9 outliers final: 4 residues processed: 421 average time/residue: 0.4578 time to fit residues: 304.2198 Evaluate side-chains 375 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 369 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 141 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN C 164 ASN C 288 ASN C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN F 474 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109737 restraints weight = 39534.618| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.19 r_work: 0.2952 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 32187 Z= 0.274 Angle : 0.603 8.318 44107 Z= 0.314 Chirality : 0.046 0.218 5442 Planarity : 0.005 0.050 5734 Dihedral : 6.006 179.856 5064 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.50 % Allowed : 8.51 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 4694 helix: 2.17 (0.11), residues: 2337 sheet: -1.85 (0.21), residues: 547 loop : -0.35 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 541 HIS 0.005 0.001 HIS A 213 PHE 0.023 0.002 PHE F 241 TYR 0.020 0.002 TYR F 28 ARG 0.005 0.001 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 2167) hydrogen bonds : angle 5.03428 ( 6309) covalent geometry : bond 0.00666 (32187) covalent geometry : angle 0.60350 (44107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 3.594 Fit side-chains REVERT: A 177 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7547 (mtm180) REVERT: B 166 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7553 (ttm-80) REVERT: C 39 ASN cc_start: 0.8771 (t0) cc_final: 0.8195 (t0) REVERT: C 485 MET cc_start: 0.8149 (mtp) cc_final: 0.7890 (mtt) REVERT: D 102 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8481 (tt) REVERT: D 108 MET cc_start: 0.8857 (mtm) cc_final: 0.8651 (mtm) REVERT: D 355 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: E 134 ASP cc_start: 0.8424 (p0) cc_final: 0.8096 (p0) REVERT: E 302 THR cc_start: 0.7712 (m) cc_final: 0.7285 (p) REVERT: E 341 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8513 (mt-10) REVERT: F 235 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8662 (mt) REVERT: K 200 ASN cc_start: 0.9015 (t0) cc_final: 0.8745 (t0) REVERT: L 82 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7941 (tm-30) outliers start: 35 outliers final: 19 residues processed: 399 average time/residue: 0.4699 time to fit residues: 297.1204 Evaluate side-chains 372 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 349 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 379 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 333 optimal weight: 9.9990 chunk 414 optimal weight: 50.0000 chunk 401 optimal weight: 40.0000 chunk 51 optimal weight: 0.9990 chunk 307 optimal weight: 0.5980 chunk 449 optimal weight: 50.0000 chunk 206 optimal weight: 0.2980 chunk 152 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 27 ASN C 164 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115930 restraints weight = 39097.963| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.39 r_work: 0.3051 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32187 Z= 0.131 Angle : 0.492 6.668 44107 Z= 0.256 Chirality : 0.042 0.200 5442 Planarity : 0.004 0.048 5734 Dihedral : 5.496 177.336 5057 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.67 % Allowed : 11.29 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4694 helix: 2.41 (0.11), residues: 2341 sheet: -1.92 (0.20), residues: 558 loop : -0.23 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 541 HIS 0.003 0.001 HIS E 450 PHE 0.016 0.001 PHE F 439 TYR 0.014 0.001 TYR B 49 ARG 0.006 0.000 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 2167) hydrogen bonds : angle 4.62916 ( 6309) covalent geometry : bond 0.00301 (32187) covalent geometry : angle 0.49183 (44107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 397 time to evaluate : 3.464 Fit side-chains REVERT: C 485 MET cc_start: 0.8142 (mtp) cc_final: 0.7907 (mtt) REVERT: D 74 ARG cc_start: 0.8402 (ttt180) cc_final: 0.8108 (ttm110) REVERT: D 161 MET cc_start: 0.8878 (mtp) cc_final: 0.8443 (mtp) REVERT: E 39 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8552 (t0) REVERT: E 134 ASP cc_start: 0.8171 (p0) cc_final: 0.7814 (p0) REVERT: E 179 ARG cc_start: 0.8583 (ptp90) cc_final: 0.8374 (ptp90) REVERT: E 240 LEU cc_start: 0.8921 (mt) cc_final: 0.8595 (mt) REVERT: E 290 MET cc_start: 0.8534 (mmt) cc_final: 0.8004 (tpp) REVERT: E 302 THR cc_start: 0.7732 (m) cc_final: 0.7412 (p) REVERT: E 445 LEU cc_start: 0.8845 (mp) cc_final: 0.8633 (mp) REVERT: F 353 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8958 (mp) REVERT: K 200 ASN cc_start: 0.8882 (t0) cc_final: 0.8554 (t0) REVERT: L 82 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8075 (tm-30) REVERT: L 103 ILE cc_start: 0.8494 (mm) cc_final: 0.8214 (mm) REVERT: M 18 MET cc_start: 0.8349 (tpp) cc_final: 0.8022 (tpt) outliers start: 39 outliers final: 20 residues processed: 418 average time/residue: 0.4478 time to fit residues: 296.9844 Evaluate side-chains 389 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 367 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 115 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 289 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 391 optimal weight: 0.4980 chunk 336 optimal weight: 40.0000 chunk 241 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 527 GLN C 164 ASN C 274 ASN C 323 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111488 restraints weight = 39433.908| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.08 r_work: 0.2926 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32187 Z= 0.152 Angle : 0.500 8.892 44107 Z= 0.258 Chirality : 0.042 0.200 5442 Planarity : 0.004 0.050 5734 Dihedral : 5.348 172.982 5053 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.27 % Allowed : 12.36 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.13), residues: 4694 helix: 2.47 (0.11), residues: 2344 sheet: -1.96 (0.20), residues: 554 loop : -0.23 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE F 439 TYR 0.014 0.001 TYR F 28 ARG 0.006 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 2167) hydrogen bonds : angle 4.51900 ( 6309) covalent geometry : bond 0.00359 (32187) covalent geometry : angle 0.49984 (44107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 3.977 Fit side-chains REVERT: A 74 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 364 LEU cc_start: 0.9103 (mp) cc_final: 0.8900 (mp) REVERT: C 485 MET cc_start: 0.8177 (mtp) cc_final: 0.7929 (mtt) REVERT: D 74 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8129 (ttm110) REVERT: D 161 MET cc_start: 0.8994 (mtp) cc_final: 0.8531 (mtp) REVERT: E 39 ASN cc_start: 0.8740 (t0) cc_final: 0.8375 (t0) REVERT: E 134 ASP cc_start: 0.8262 (p0) cc_final: 0.7910 (p0) REVERT: E 290 MET cc_start: 0.8576 (mmt) cc_final: 0.8001 (tpp) REVERT: E 302 THR cc_start: 0.7766 (m) cc_final: 0.7459 (p) REVERT: E 486 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8074 (mttm) REVERT: F 235 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8549 (mt) REVERT: K 152 MET cc_start: 0.8878 (ptp) cc_final: 0.8608 (ptm) REVERT: K 200 ASN cc_start: 0.8977 (t0) cc_final: 0.8713 (t0) REVERT: L 82 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7787 (tm-30) REVERT: L 103 ILE cc_start: 0.8374 (mm) cc_final: 0.8061 (mm) REVERT: M 18 MET cc_start: 0.8342 (tpp) cc_final: 0.7984 (tpt) outliers start: 53 outliers final: 31 residues processed: 412 average time/residue: 0.4558 time to fit residues: 299.3395 Evaluate side-chains 395 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 361 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 163 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 270 optimal weight: 0.5980 chunk 300 optimal weight: 0.7980 chunk 381 optimal weight: 2.9990 chunk 443 optimal weight: 50.0000 chunk 4 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110803 restraints weight = 39221.889| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.43 r_work: 0.2987 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32187 Z= 0.219 Angle : 0.551 8.926 44107 Z= 0.283 Chirality : 0.044 0.196 5442 Planarity : 0.004 0.050 5734 Dihedral : 5.490 173.225 5053 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.65 % Allowed : 13.34 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4694 helix: 2.42 (0.11), residues: 2336 sheet: -2.07 (0.20), residues: 564 loop : -0.32 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.005 0.001 HIS A 213 PHE 0.017 0.001 PHE F 439 TYR 0.017 0.002 TYR F 28 ARG 0.006 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 2167) hydrogen bonds : angle 4.59268 ( 6309) covalent geometry : bond 0.00530 (32187) covalent geometry : angle 0.55060 (44107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 3.633 Fit side-chains REVERT: A 74 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: A 177 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7444 (mtm180) REVERT: A 234 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 300 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8438 (mt) REVERT: B 166 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7630 (ttm-80) REVERT: B 364 LEU cc_start: 0.9088 (mp) cc_final: 0.8884 (mp) REVERT: C 39 ASN cc_start: 0.8701 (t0) cc_final: 0.8369 (t0) REVERT: C 272 TYR cc_start: 0.8349 (m-80) cc_final: 0.8000 (m-80) REVERT: C 485 MET cc_start: 0.8214 (mtp) cc_final: 0.7954 (mtt) REVERT: D 74 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8134 (ttm110) REVERT: D 355 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: E 39 ASN cc_start: 0.8882 (t0) cc_final: 0.8534 (t0) REVERT: E 134 ASP cc_start: 0.8442 (p0) cc_final: 0.8058 (p0) REVERT: E 240 LEU cc_start: 0.8957 (mt) cc_final: 0.8660 (mt) REVERT: E 302 THR cc_start: 0.7830 (m) cc_final: 0.7531 (p) REVERT: E 531 TYR cc_start: 0.8993 (m-80) cc_final: 0.8686 (m-80) REVERT: F 235 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (mt) REVERT: F 308 MET cc_start: 0.8939 (ttp) cc_final: 0.8661 (ttp) REVERT: L 82 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7696 (tm-30) REVERT: L 103 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8141 (mm) REVERT: M 18 MET cc_start: 0.8353 (tpp) cc_final: 0.8030 (tpt) outliers start: 62 outliers final: 40 residues processed: 412 average time/residue: 0.4828 time to fit residues: 316.1208 Evaluate side-chains 399 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 270 optimal weight: 0.1980 chunk 251 optimal weight: 1.9990 chunk 440 optimal weight: 40.0000 chunk 17 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 412 optimal weight: 20.0000 chunk 410 optimal weight: 3.9990 chunk 401 optimal weight: 40.0000 chunk 419 optimal weight: 50.0000 chunk 352 optimal weight: 1.9990 chunk 276 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A 554 HIS B 27 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 455 ASN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110107 restraints weight = 39517.568| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.77 r_work: 0.2950 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32187 Z= 0.195 Angle : 0.532 7.352 44107 Z= 0.274 Chirality : 0.043 0.193 5442 Planarity : 0.004 0.050 5734 Dihedral : 5.459 172.872 5053 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.95 % Allowed : 14.11 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4694 helix: 2.45 (0.11), residues: 2331 sheet: -2.12 (0.19), residues: 573 loop : -0.32 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.001 PHE F 439 TYR 0.016 0.001 TYR F 28 ARG 0.005 0.000 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 2167) hydrogen bonds : angle 4.55475 ( 6309) covalent geometry : bond 0.00471 (32187) covalent geometry : angle 0.53150 (44107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 7.778 Fit side-chains REVERT: A 74 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: A 177 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7410 (mtm180) REVERT: A 234 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 166 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7656 (ttm-80) REVERT: B 337 MET cc_start: 0.8495 (mtp) cc_final: 0.8265 (mtm) REVERT: B 364 LEU cc_start: 0.9075 (mp) cc_final: 0.8864 (mp) REVERT: C 39 ASN cc_start: 0.8770 (t0) cc_final: 0.8360 (t0) REVERT: C 45 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: C 485 MET cc_start: 0.8222 (mtp) cc_final: 0.7959 (mtt) REVERT: D 74 ARG cc_start: 0.8510 (ttt180) cc_final: 0.8153 (ttm110) REVERT: D 355 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: E 39 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8552 (t0) REVERT: E 134 ASP cc_start: 0.8467 (p0) cc_final: 0.8092 (p0) REVERT: E 240 LEU cc_start: 0.8959 (mt) cc_final: 0.8654 (mt) REVERT: E 302 THR cc_start: 0.7858 (m) cc_final: 0.7571 (p) REVERT: E 486 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: E 531 TYR cc_start: 0.9009 (m-80) cc_final: 0.8708 (m-80) REVERT: F 235 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8603 (mt) REVERT: F 315 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (mp) REVERT: J 101 THR cc_start: 0.9205 (m) cc_final: 0.8977 (p) REVERT: L 82 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7718 (tm-30) REVERT: L 103 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8169 (mm) REVERT: M 18 MET cc_start: 0.8298 (tpp) cc_final: 0.7987 (tpt) outliers start: 69 outliers final: 47 residues processed: 411 average time/residue: 0.7419 time to fit residues: 508.5999 Evaluate side-chains 414 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 204 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 350 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 148 optimal weight: 0.0050 chunk 157 optimal weight: 5.9990 chunk 462 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 27 ASN D 331 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 455 ASN F 186 GLN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113130 restraints weight = 39107.646| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.73 r_work: 0.3015 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32187 Z= 0.132 Angle : 0.489 7.336 44107 Z= 0.253 Chirality : 0.042 0.180 5442 Planarity : 0.004 0.049 5734 Dihedral : 5.259 167.795 5053 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.74 % Allowed : 15.18 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.13), residues: 4694 helix: 2.58 (0.11), residues: 2330 sheet: -2.05 (0.20), residues: 567 loop : -0.27 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 541 HIS 0.003 0.001 HIS F 344 PHE 0.016 0.001 PHE F 439 TYR 0.014 0.001 TYR D 284 ARG 0.006 0.000 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 2167) hydrogen bonds : angle 4.42378 ( 6309) covalent geometry : bond 0.00307 (32187) covalent geometry : angle 0.48942 (44107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 383 time to evaluate : 3.520 Fit side-chains REVERT: A 74 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: A 234 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8487 (mt) REVERT: A 300 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 166 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7728 (ttm-80) REVERT: B 364 LEU cc_start: 0.9072 (mp) cc_final: 0.8849 (mp) REVERT: C 39 ASN cc_start: 0.8739 (t0) cc_final: 0.8334 (t0) REVERT: C 45 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: C 432 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8406 (mp) REVERT: D 74 ARG cc_start: 0.8456 (ttt180) cc_final: 0.8169 (ttm110) REVERT: D 304 TYR cc_start: 0.9398 (m-80) cc_final: 0.9192 (m-80) REVERT: E 39 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8510 (t0) REVERT: E 134 ASP cc_start: 0.8366 (p0) cc_final: 0.7957 (p0) REVERT: E 240 LEU cc_start: 0.8934 (mt) cc_final: 0.8620 (mt) REVERT: E 483 ASP cc_start: 0.8772 (m-30) cc_final: 0.8546 (m-30) REVERT: E 486 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7996 (mttm) REVERT: E 531 TYR cc_start: 0.9005 (m-80) cc_final: 0.8693 (m-80) REVERT: F 235 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8507 (mt) REVERT: L 82 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7708 (tm-30) REVERT: L 103 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8138 (mm) REVERT: M 18 MET cc_start: 0.8254 (tpp) cc_final: 0.7934 (tpt) outliers start: 64 outliers final: 41 residues processed: 427 average time/residue: 0.4529 time to fit residues: 308.0065 Evaluate side-chains 414 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 390 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 400 optimal weight: 40.0000 chunk 276 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 414 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 27 ASN C 164 ASN C 248 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN F 186 GLN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118945 restraints weight = 39010.959| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.46 r_work: 0.3015 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32187 Z= 0.168 Angle : 0.516 8.012 44107 Z= 0.265 Chirality : 0.043 0.176 5442 Planarity : 0.004 0.047 5734 Dihedral : 5.256 164.602 5053 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.78 % Allowed : 15.74 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.13), residues: 4694 helix: 2.56 (0.11), residues: 2331 sheet: -2.02 (0.20), residues: 568 loop : -0.27 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.001 PHE F 439 TYR 0.016 0.001 TYR C 212 ARG 0.006 0.000 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 2167) hydrogen bonds : angle 4.43441 ( 6309) covalent geometry : bond 0.00403 (32187) covalent geometry : angle 0.51568 (44107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 3.307 Fit side-chains REVERT: A 74 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: A 177 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7354 (mtm180) REVERT: A 234 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8525 (mt) REVERT: A 300 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 166 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7729 (ttm-80) REVERT: B 364 LEU cc_start: 0.9084 (mp) cc_final: 0.8862 (mp) REVERT: C 39 ASN cc_start: 0.8726 (t0) cc_final: 0.8372 (t0) REVERT: C 45 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8050 (ttt) REVERT: D 74 ARG cc_start: 0.8455 (ttt180) cc_final: 0.8162 (ttm110) REVERT: D 304 TYR cc_start: 0.9415 (m-80) cc_final: 0.9207 (m-80) REVERT: E 39 ASN cc_start: 0.8807 (t0) cc_final: 0.8500 (t0) REVERT: E 173 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9206 (mt) REVERT: E 240 LEU cc_start: 0.8909 (mt) cc_final: 0.8611 (mt) REVERT: E 486 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7998 (mttm) REVERT: F 235 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8562 (mt) REVERT: K 219 ARG cc_start: 0.8857 (ttt180) cc_final: 0.8478 (ttm-80) REVERT: L 82 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7733 (tm-30) REVERT: L 103 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8190 (mm) REVERT: M 18 MET cc_start: 0.8266 (tpp) cc_final: 0.7920 (tpt) outliers start: 65 outliers final: 47 residues processed: 412 average time/residue: 0.4949 time to fit residues: 325.3908 Evaluate side-chains 421 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 365 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 241 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 372 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 chunk 289 optimal weight: 0.2980 chunk 367 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 27 ASN C 164 ASN C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 455 ASN F 186 GLN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119510 restraints weight = 38875.943| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.43 r_work: 0.3073 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32187 Z= 0.134 Angle : 0.498 10.604 44107 Z= 0.256 Chirality : 0.042 0.181 5442 Planarity : 0.004 0.047 5734 Dihedral : 5.128 159.200 5053 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.61 % Allowed : 16.00 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4694 helix: 2.61 (0.11), residues: 2332 sheet: -1.97 (0.20), residues: 567 loop : -0.24 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.003 0.001 HIS F 344 PHE 0.016 0.001 PHE F 439 TYR 0.013 0.001 TYR C 212 ARG 0.006 0.000 ARG I 166 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 2167) hydrogen bonds : angle 4.37911 ( 6309) covalent geometry : bond 0.00314 (32187) covalent geometry : angle 0.49821 (44107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 374 time to evaluate : 3.551 Fit side-chains REVERT: A 74 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: A 177 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7329 (mtm180) REVERT: A 234 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 166 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7759 (ttm-80) REVERT: B 364 LEU cc_start: 0.9084 (mp) cc_final: 0.8854 (mp) REVERT: C 39 ASN cc_start: 0.8687 (t0) cc_final: 0.8342 (t0) REVERT: C 45 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7968 (ttt) REVERT: C 547 MET cc_start: 0.8414 (ttp) cc_final: 0.8213 (mtp) REVERT: D 74 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8154 (ttm110) REVERT: D 304 TYR cc_start: 0.9396 (m-80) cc_final: 0.9189 (m-80) REVERT: E 39 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8467 (t0) REVERT: E 173 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9188 (mt) REVERT: E 486 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: F 235 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8528 (mt) REVERT: K 219 ARG cc_start: 0.8815 (ttt180) cc_final: 0.8504 (ttm-80) REVERT: L 82 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7748 (tm-30) REVERT: L 103 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8186 (mm) REVERT: M 18 MET cc_start: 0.8237 (tpp) cc_final: 0.7912 (tpt) outliers start: 61 outliers final: 46 residues processed: 411 average time/residue: 0.4521 time to fit residues: 295.4590 Evaluate side-chains 420 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 365 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 72 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 421 optimal weight: 40.0000 chunk 235 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 466 optimal weight: 30.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN C 164 ASN C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 346 GLN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113002 restraints weight = 39392.766| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.34 r_work: 0.2885 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 32187 Z= 0.334 Angle : 0.646 11.885 44107 Z= 0.333 Chirality : 0.048 0.232 5442 Planarity : 0.005 0.051 5734 Dihedral : 5.561 165.029 5053 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 16.12 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4694 helix: 2.29 (0.11), residues: 2321 sheet: -2.13 (0.21), residues: 538 loop : -0.49 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 541 HIS 0.008 0.002 HIS A 213 PHE 0.018 0.002 PHE M 43 TYR 0.026 0.002 TYR C 212 ARG 0.006 0.001 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 2167) hydrogen bonds : angle 4.68350 ( 6309) covalent geometry : bond 0.00818 (32187) covalent geometry : angle 0.64622 (44107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 3.365 Fit side-chains REVERT: A 74 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: A 177 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7574 (mtm180) REVERT: A 234 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 300 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 166 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7816 (ttm-80) REVERT: B 364 LEU cc_start: 0.9103 (mp) cc_final: 0.8889 (mp) REVERT: C 39 ASN cc_start: 0.8899 (t0) cc_final: 0.8511 (t0) REVERT: D 74 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8181 (ttm110) REVERT: D 355 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: E 39 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8536 (t0) REVERT: E 134 ASP cc_start: 0.8551 (p0) cc_final: 0.8036 (p0) REVERT: E 173 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9226 (mt) REVERT: E 240 LEU cc_start: 0.8940 (mt) cc_final: 0.8657 (mt) REVERT: E 341 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 486 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8251 (mttm) REVERT: F 235 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (mt) REVERT: F 315 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9009 (mp) REVERT: L 82 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7683 (tm-30) REVERT: L 103 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8252 (mm) REVERT: M 18 MET cc_start: 0.8278 (tpp) cc_final: 0.7997 (tpt) outliers start: 64 outliers final: 45 residues processed: 395 average time/residue: 0.4613 time to fit residues: 289.4956 Evaluate side-chains 402 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 346 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 186 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 359 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 418 optimal weight: 50.0000 chunk 118 optimal weight: 0.9990 chunk 459 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN C 164 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114896 restraints weight = 39144.995| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.75 r_work: 0.2910 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 32187 Z= 0.273 Angle : 0.862 59.200 44107 Z= 0.489 Chirality : 0.045 0.279 5442 Planarity : 0.005 0.142 5734 Dihedral : 5.569 165.254 5053 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.48 % Allowed : 16.55 % Favored : 80.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4694 helix: 2.31 (0.11), residues: 2321 sheet: -2.17 (0.20), residues: 538 loop : -0.50 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 541 HIS 0.006 0.001 HIS A 213 PHE 0.016 0.002 PHE F 439 TYR 0.021 0.002 TYR C 212 ARG 0.005 0.000 ARG I 166 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 2167) hydrogen bonds : angle 4.68347 ( 6309) covalent geometry : bond 0.00643 (32187) covalent geometry : angle 0.86245 (44107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17883.12 seconds wall clock time: 311 minutes 11.44 seconds (18671.44 seconds total)