Starting phenix.real_space_refine on Sat Feb 17 17:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbj_7075/02_2024/6bbj_7075.pdb" } resolution = 3.8 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= 0.037 sd= 0.456 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 12752 2.51 5 N 3196 2.21 5 O 3424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 612": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 311": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 612": "NH1" <-> "NH2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C ARG 612": "NH1" <-> "NH2" Residue "C ARG 749": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ARG 612": "NH1" <-> "NH2" Residue "D ARG 749": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19496 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4874 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4874 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4874 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4874 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 10.02, per 1000 atoms: 0.51 Number of scatterers: 19496 At special positions: 0 Unit cell: (142.528, 142.528, 121.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3424 8.00 N 3196 7.00 C 12752 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 - 3.50 Amino acid : False - 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: 7.18 Conformation dependent library (CDL) restraints added in 3.6 seconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 64.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU A 163 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.818A pdb=" N MET A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 252 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.539A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.695A pdb=" N ILE A 361 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 removed outlier: 3.898A pdb=" N ALA A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 375 " --> pdb=" O MET A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS A 397 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 4.509A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 590 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 715 removed outlier: 4.076A pdb=" N ILE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU B 163 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 302 " --> pdb=" O HIS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.645A pdb=" N ALA B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.696A pdb=" N ILE B 361 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 377 removed outlier: 3.899A pdb=" N ALA B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.632A pdb=" N ARG B 396 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 removed outlier: 3.641A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 448 through 486 removed outlier: 3.857A pdb=" N GLU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 509 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 516 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 563 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 removed outlier: 4.508A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR B 589 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 590 " --> pdb=" O TYR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU B 602 " --> pdb=" O TYR B 598 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 605 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 715 removed outlier: 4.075A pdb=" N ILE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 744 " --> pdb=" O ILE B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.822A pdb=" N GLU C 163 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 removed outlier: 3.500A pdb=" N ILE C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.611A pdb=" N GLU C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 252 " --> pdb=" O HIS C 248 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.060A pdb=" N VAL C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 302 " --> pdb=" O HIS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.696A pdb=" N ILE C 361 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 removed outlier: 3.898A pdb=" N ALA C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG C 396 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS C 397 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 436 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 477 " --> pdb=" O SER C 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 510 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 515 " --> pdb=" O ILE C 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 516 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN C 524 " --> pdb=" O PHE C 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 566 removed outlier: 3.951A pdb=" N LEU C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 563 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 4.508A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 582 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR C 589 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG C 590 " --> pdb=" O TYR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU C 602 " --> pdb=" O TYR C 598 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 605 " --> pdb=" O MET C 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 672 " --> pdb=" O ASP C 668 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 715 removed outlier: 4.075A pdb=" N ILE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE C 737 " --> pdb=" O TRP C 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 744 " --> pdb=" O ILE C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU D 163 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.685A pdb=" N LEU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.984A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 252 " --> pdb=" O HIS D 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU D 302 " --> pdb=" O HIS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 338 " --> pdb=" O ASN D 334 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 346 " --> pdb=" O TYR D 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.695A pdb=" N ILE D 361 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 removed outlier: 3.899A pdb=" N ALA D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG D 396 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS D 397 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 509 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 510 " --> pdb=" O ARG D 506 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 515 " --> pdb=" O ILE D 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 516 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN D 524 " --> pdb=" O PHE D 520 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU D 547 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 584 removed outlier: 4.509A pdb=" N VAL D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP D 582 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 590 removed outlier: 3.757A pdb=" N THR D 589 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 590 " --> pdb=" O TYR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU D 602 " --> pdb=" O TYR D 598 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 605 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 631 " --> pdb=" O ALA D 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 675 removed outlier: 3.699A pdb=" N LYS D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 715 removed outlier: 4.076A pdb=" N ILE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET D 709 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 725 Processing helix chain 'D' and resid 727 through 744 removed outlier: 3.801A pdb=" N ILE D 737 " --> pdb=" O TRP D 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 744 " --> pdb=" O ILE D 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 407 removed outlier: 6.893A pdb=" N SER A 412 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA A 406 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 771 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER B 412 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 406 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 771 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER C 412 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C 406 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 771 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER D 412 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D 406 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 771 " --> pdb=" O VAL D 758 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2472 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: 5.24 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6026 1.34 - 1.46: 4421 1.46 - 1.58: 9261 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 19924 Sorted by residual: bond pdb=" C GLU C 449 " pdb=" N PRO C 450 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.55e+00 bond pdb=" C GLU D 449 " pdb=" N PRO D 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 bond pdb=" C GLU A 449 " pdb=" N PRO A 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" C GLU B 449 " pdb=" N PRO B 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C ASN D 633 " pdb=" N PRO D 634 " ideal model delta sigma weight residual 1.328 1.344 -0.015 1.26e-02 6.30e+03 1.50e+00 ... (remaining 19919 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 393 106.25 - 113.18: 10704 113.18 - 120.11: 7548 120.11 - 127.04: 8141 127.04 - 133.97: 178 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C GLN B 172 " pdb=" N LYS B 173 " pdb=" CA LYS B 173 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C GLN C 172 " pdb=" N LYS C 173 " pdb=" CA LYS C 173 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C GLN A 172 " pdb=" N LYS A 173 " pdb=" CA LYS A 173 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLN D 172 " pdb=" N LYS D 173 " pdb=" CA LYS D 173 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C THR B 717 " pdb=" N VAL B 718 " pdb=" CA VAL B 718 " ideal model delta sigma weight residual 122.97 119.28 3.69 9.80e-01 1.04e+00 1.42e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.65: 10638 9.65 - 19.30: 966 19.30 - 28.95: 124 28.95 - 38.59: 52 38.59 - 48.24: 40 Dihedral angle restraints: 11820 sinusoidal: 4688 harmonic: 7132 Sorted by residual: dihedral pdb=" CA VAL A 561 " pdb=" C VAL A 561 " pdb=" N LEU A 562 " pdb=" CA LEU A 562 " ideal model delta harmonic sigma weight residual 180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL C 561 " pdb=" C VAL C 561 " pdb=" N LEU C 562 " pdb=" CA LEU C 562 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL B 561 " pdb=" C VAL B 561 " pdb=" N LEU B 562 " pdb=" CA LEU B 562 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 11817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1985 0.038 - 0.076: 907 0.076 - 0.113: 168 0.113 - 0.151: 40 0.151 - 0.189: 8 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA GLU C 449 " pdb=" N GLU C 449 " pdb=" C GLU C 449 " pdb=" CB GLU C 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA GLU B 449 " pdb=" N GLU B 449 " pdb=" C GLU B 449 " pdb=" CB GLU B 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLU A 449 " pdb=" N GLU A 449 " pdb=" C GLU A 449 " pdb=" CB GLU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 3105 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 408 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 409 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 408 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 409 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 408 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 409 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 409 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 409 " 0.023 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 6558 2.87 - 3.37: 18485 3.37 - 3.88: 30936 3.88 - 4.39: 35137 4.39 - 4.90: 58888 Nonbonded interactions: 150004 Sorted by model distance: nonbonded pdb=" O ASP A 152 " pdb=" OG SER A 155 " model vdw 2.358 2.440 nonbonded pdb=" O ASP B 152 " pdb=" OG SER B 155 " model vdw 2.358 2.440 nonbonded pdb=" O ASP D 152 " pdb=" OG SER D 155 " model vdw 2.358 2.440 nonbonded pdb=" O ASP C 152 " pdb=" OG SER C 155 " model vdw 2.359 2.440 nonbonded pdb=" O PHE C 467 " pdb=" OG SER C 470 " model vdw 2.361 2.440 ... (remaining 149999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.480 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 49.270 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19924 Z= 0.221 Angle : 0.726 8.951 26964 Z= 0.403 Chirality : 0.044 0.189 3108 Planarity : 0.005 0.042 3324 Dihedral : 8.257 48.242 7220 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.19 % Allowed : 1.33 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -5.00 (0.12), residues: 2400 helix: -3.84 (0.07), residues: 1284 sheet: -2.85 (0.47), residues: 84 loop : -2.42 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 772 HIS 0.008 0.001 HIS C 298 PHE 0.017 0.002 PHE C 337 TYR 0.028 0.002 TYR B 687 ARG 0.004 0.001 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 927 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8206 (p) cc_final: 0.7872 (t) REVERT: A 209 LEU cc_start: 0.8924 (mt) cc_final: 0.8704 (mt) REVERT: A 222 PHE cc_start: 0.7200 (t80) cc_final: 0.6179 (t80) REVERT: A 381 ILE cc_start: 0.8922 (tp) cc_final: 0.8631 (mm) REVERT: A 584 ASN cc_start: 0.8751 (m-40) cc_final: 0.8531 (m110) REVERT: A 615 LEU cc_start: 0.9206 (mt) cc_final: 0.8398 (tp) REVERT: A 619 LEU cc_start: 0.9376 (mt) cc_final: 0.9018 (mt) REVERT: A 630 SER cc_start: 0.9082 (m) cc_final: 0.8798 (p) REVERT: B 181 PHE cc_start: 0.7510 (m-80) cc_final: 0.7240 (m-80) REVERT: B 186 THR cc_start: 0.8152 (p) cc_final: 0.7798 (t) REVERT: B 209 LEU cc_start: 0.8951 (mt) cc_final: 0.8701 (mt) REVERT: B 222 PHE cc_start: 0.7381 (t80) cc_final: 0.6172 (t80) REVERT: B 299 TYR cc_start: 0.7972 (t80) cc_final: 0.7742 (t80) REVERT: B 381 ILE cc_start: 0.8914 (tp) cc_final: 0.8613 (mm) REVERT: B 393 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 584 ASN cc_start: 0.8894 (m-40) cc_final: 0.8629 (m110) REVERT: B 615 LEU cc_start: 0.9223 (mt) cc_final: 0.8460 (tp) REVERT: B 619 LEU cc_start: 0.9354 (mt) cc_final: 0.9089 (mt) REVERT: B 630 SER cc_start: 0.9129 (m) cc_final: 0.8868 (p) REVERT: C 181 PHE cc_start: 0.7452 (m-80) cc_final: 0.7202 (m-80) REVERT: C 186 THR cc_start: 0.8073 (p) cc_final: 0.7721 (t) REVERT: C 209 LEU cc_start: 0.8939 (mt) cc_final: 0.8673 (mt) REVERT: C 222 PHE cc_start: 0.7364 (t80) cc_final: 0.6205 (t80) REVERT: C 381 ILE cc_start: 0.8896 (tp) cc_final: 0.8688 (mm) REVERT: C 615 LEU cc_start: 0.9241 (mt) cc_final: 0.9024 (mt) REVERT: C 630 SER cc_start: 0.9418 (m) cc_final: 0.9164 (p) REVERT: C 693 ILE cc_start: 0.8944 (pt) cc_final: 0.8688 (tp) REVERT: D 181 PHE cc_start: 0.7695 (m-80) cc_final: 0.7393 (m-80) REVERT: D 186 THR cc_start: 0.7978 (p) cc_final: 0.7615 (t) REVERT: D 209 LEU cc_start: 0.8977 (mt) cc_final: 0.8733 (mt) REVERT: D 222 PHE cc_start: 0.7569 (t80) cc_final: 0.6318 (t80) REVERT: D 299 TYR cc_start: 0.8151 (t80) cc_final: 0.7936 (t80) REVERT: D 381 ILE cc_start: 0.8865 (tp) cc_final: 0.8615 (mm) REVERT: D 387 ARG cc_start: 0.8300 (mpp80) cc_final: 0.7987 (mtm-85) REVERT: D 393 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 520 PHE cc_start: 0.8808 (t80) cc_final: 0.8594 (t80) REVERT: D 522 ILE cc_start: 0.8845 (mm) cc_final: 0.8630 (tp) REVERT: D 584 ASN cc_start: 0.9118 (m-40) cc_final: 0.8806 (m110) REVERT: D 615 LEU cc_start: 0.9152 (mt) cc_final: 0.8555 (tp) REVERT: D 619 LEU cc_start: 0.9381 (mt) cc_final: 0.9157 (mt) REVERT: D 630 SER cc_start: 0.9301 (m) cc_final: 0.9080 (p) REVERT: D 667 LEU cc_start: 0.8684 (tp) cc_final: 0.8440 (tp) outliers start: 4 outliers final: 0 residues processed: 931 average time/residue: 0.3013 time to fit residues: 422.4461 Evaluate side-chains 528 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 218 ASN A 239 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 239 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 239 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 727 GLN D 239 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19924 Z= 0.197 Angle : 0.615 7.753 26964 Z= 0.319 Chirality : 0.041 0.168 3108 Planarity : 0.004 0.041 3324 Dihedral : 4.323 15.026 2656 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.41 % Allowed : 13.47 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.73 (0.15), residues: 2400 helix: -1.59 (0.11), residues: 1412 sheet: -1.59 (0.50), residues: 76 loop : -1.97 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 772 HIS 0.006 0.001 HIS B 443 PHE 0.025 0.002 PHE A 545 TYR 0.019 0.001 TYR D 232 ARG 0.006 0.001 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 586 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8095 (p) cc_final: 0.7735 (t) REVERT: A 423 CYS cc_start: 0.7196 (t) cc_final: 0.6438 (p) REVERT: A 520 PHE cc_start: 0.8697 (t80) cc_final: 0.8368 (t80) REVERT: A 553 SER cc_start: 0.9547 (m) cc_final: 0.9178 (p) REVERT: A 609 ASP cc_start: 0.7537 (m-30) cc_final: 0.7051 (t70) REVERT: A 614 LEU cc_start: 0.9209 (tp) cc_final: 0.8980 (tp) REVERT: A 615 LEU cc_start: 0.9091 (mt) cc_final: 0.8587 (tp) REVERT: A 630 SER cc_start: 0.9140 (m) cc_final: 0.8928 (p) REVERT: A 703 PHE cc_start: 0.8742 (t80) cc_final: 0.8393 (t80) REVERT: A 709 MET cc_start: 0.8592 (mmt) cc_final: 0.8369 (mmt) REVERT: B 186 THR cc_start: 0.8139 (p) cc_final: 0.7764 (t) REVERT: B 222 PHE cc_start: 0.7592 (t80) cc_final: 0.7358 (t80) REVERT: B 459 TRP cc_start: 0.8751 (t-100) cc_final: 0.8532 (t-100) REVERT: B 520 PHE cc_start: 0.8786 (t80) cc_final: 0.8461 (t80) REVERT: B 553 SER cc_start: 0.9629 (m) cc_final: 0.9226 (p) REVERT: B 609 ASP cc_start: 0.7726 (m-30) cc_final: 0.7171 (t70) REVERT: B 615 LEU cc_start: 0.9043 (mt) cc_final: 0.8572 (tp) REVERT: B 703 PHE cc_start: 0.8806 (t80) cc_final: 0.8442 (t80) REVERT: C 186 THR cc_start: 0.7978 (p) cc_final: 0.7593 (t) REVERT: C 520 PHE cc_start: 0.9101 (t80) cc_final: 0.8439 (t80) REVERT: C 553 SER cc_start: 0.9705 (m) cc_final: 0.9282 (p) REVERT: C 584 ASN cc_start: 0.8767 (m110) cc_final: 0.8176 (m110) REVERT: C 609 ASP cc_start: 0.7751 (m-30) cc_final: 0.7197 (t70) REVERT: C 628 LEU cc_start: 0.9256 (mt) cc_final: 0.8784 (mm) REVERT: C 665 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8588 (t80) REVERT: C 703 PHE cc_start: 0.8871 (t80) cc_final: 0.8587 (t80) REVERT: C 737 ILE cc_start: 0.9311 (tp) cc_final: 0.9026 (tp) REVERT: D 186 THR cc_start: 0.7827 (p) cc_final: 0.7411 (t) REVERT: D 209 LEU cc_start: 0.9037 (mt) cc_final: 0.8797 (mt) REVERT: D 222 PHE cc_start: 0.7780 (t80) cc_final: 0.7498 (t80) REVERT: D 283 LEU cc_start: 0.9216 (mm) cc_final: 0.9008 (mm) REVERT: D 520 PHE cc_start: 0.8986 (t80) cc_final: 0.8552 (t80) REVERT: D 553 SER cc_start: 0.9707 (m) cc_final: 0.9313 (p) REVERT: D 609 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7406 (t70) REVERT: D 615 LEU cc_start: 0.8967 (mt) cc_final: 0.8661 (tp) REVERT: D 618 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8987 (mm) REVERT: D 668 ASP cc_start: 0.8115 (m-30) cc_final: 0.6748 (m-30) REVERT: D 698 TYR cc_start: 0.8512 (t80) cc_final: 0.8060 (t80) outliers start: 93 outliers final: 42 residues processed: 644 average time/residue: 0.2805 time to fit residues: 285.4423 Evaluate side-chains 517 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 472 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 218 ASN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19924 Z= 0.168 Angle : 0.571 10.126 26964 Z= 0.287 Chirality : 0.040 0.220 3108 Planarity : 0.003 0.033 3324 Dihedral : 4.105 14.600 2656 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.88 % Allowed : 16.18 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.51 (0.16), residues: 2400 helix: -0.41 (0.13), residues: 1396 sheet: -1.64 (0.49), residues: 76 loop : -1.75 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 729 HIS 0.005 0.001 HIS B 443 PHE 0.017 0.001 PHE A 168 TYR 0.024 0.001 TYR B 299 ARG 0.006 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 543 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8031 (p) cc_final: 0.7685 (t) REVERT: A 283 LEU cc_start: 0.9042 (mm) cc_final: 0.8798 (mm) REVERT: A 423 CYS cc_start: 0.6933 (t) cc_final: 0.6712 (p) REVERT: A 507 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8122 (mt) REVERT: A 520 PHE cc_start: 0.8849 (t80) cc_final: 0.8648 (t80) REVERT: A 609 ASP cc_start: 0.7467 (m-30) cc_final: 0.7219 (t70) REVERT: A 614 LEU cc_start: 0.9217 (tp) cc_final: 0.8980 (tp) REVERT: A 615 LEU cc_start: 0.9006 (mt) cc_final: 0.8742 (tp) REVERT: A 628 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8124 (mm) REVERT: A 665 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8459 (t80) REVERT: A 668 ASP cc_start: 0.8346 (m-30) cc_final: 0.8004 (m-30) REVERT: A 694 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8970 (mm) REVERT: A 703 PHE cc_start: 0.8835 (t80) cc_final: 0.8530 (t80) REVERT: A 706 LEU cc_start: 0.8932 (mt) cc_final: 0.8701 (tp) REVERT: A 727 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: A 750 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7982 (mmtt) REVERT: B 154 VAL cc_start: 0.9326 (m) cc_final: 0.9048 (p) REVERT: B 181 PHE cc_start: 0.7578 (m-80) cc_final: 0.7356 (m-80) REVERT: B 186 THR cc_start: 0.8107 (p) cc_final: 0.7733 (t) REVERT: B 283 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8915 (mm) REVERT: B 520 PHE cc_start: 0.8885 (t80) cc_final: 0.8573 (t80) REVERT: B 553 SER cc_start: 0.9559 (m) cc_final: 0.9189 (p) REVERT: B 609 ASP cc_start: 0.7764 (m-30) cc_final: 0.7324 (t0) REVERT: B 628 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 665 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8478 (t80) REVERT: B 694 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 698 TYR cc_start: 0.8568 (t80) cc_final: 0.8194 (t80) REVERT: B 703 PHE cc_start: 0.8891 (t80) cc_final: 0.8488 (t80) REVERT: B 706 LEU cc_start: 0.8902 (mt) cc_final: 0.8656 (tp) REVERT: B 727 GLN cc_start: 0.7063 (pt0) cc_final: 0.6735 (pm20) REVERT: C 154 VAL cc_start: 0.9378 (m) cc_final: 0.9124 (p) REVERT: C 186 THR cc_start: 0.7901 (p) cc_final: 0.7507 (t) REVERT: C 222 PHE cc_start: 0.7382 (t80) cc_final: 0.7154 (t80) REVERT: C 283 LEU cc_start: 0.9022 (mm) cc_final: 0.8754 (mm) REVERT: C 507 LEU cc_start: 0.8794 (tp) cc_final: 0.8462 (mt) REVERT: C 520 PHE cc_start: 0.9141 (t80) cc_final: 0.8625 (t80) REVERT: C 553 SER cc_start: 0.9709 (m) cc_final: 0.9241 (p) REVERT: C 584 ASN cc_start: 0.8727 (m110) cc_final: 0.8158 (m110) REVERT: C 609 ASP cc_start: 0.7748 (m-30) cc_final: 0.7397 (t0) REVERT: C 615 LEU cc_start: 0.9201 (mt) cc_final: 0.8891 (tp) REVERT: C 628 LEU cc_start: 0.9215 (mt) cc_final: 0.8981 (mm) REVERT: C 668 ASP cc_start: 0.8414 (m-30) cc_final: 0.7174 (m-30) REVERT: C 698 TYR cc_start: 0.8633 (t80) cc_final: 0.8184 (t80) REVERT: C 703 PHE cc_start: 0.8902 (t80) cc_final: 0.8638 (t80) REVERT: C 727 GLN cc_start: 0.7207 (pt0) cc_final: 0.6988 (pm20) REVERT: D 151 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7688 (t80) REVERT: D 181 PHE cc_start: 0.7873 (m-80) cc_final: 0.7638 (m-80) REVERT: D 186 THR cc_start: 0.7740 (p) cc_final: 0.7316 (t) REVERT: D 209 LEU cc_start: 0.9053 (mt) cc_final: 0.8843 (mt) REVERT: D 222 PHE cc_start: 0.7515 (t80) cc_final: 0.7273 (t80) REVERT: D 283 LEU cc_start: 0.9161 (mm) cc_final: 0.8740 (mm) REVERT: D 453 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7961 (mp0) REVERT: D 520 PHE cc_start: 0.8939 (t80) cc_final: 0.8591 (t80) REVERT: D 553 SER cc_start: 0.9610 (m) cc_final: 0.9263 (p) REVERT: D 609 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7788 (t0) REVERT: D 615 LEU cc_start: 0.8996 (mt) cc_final: 0.8754 (tp) REVERT: D 698 TYR cc_start: 0.8517 (t80) cc_final: 0.8126 (t80) REVERT: D 700 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8768 (tt) REVERT: D 703 PHE cc_start: 0.8878 (t80) cc_final: 0.8583 (t80) REVERT: D 727 GLN cc_start: 0.7056 (pt0) cc_final: 0.6700 (pm20) outliers start: 124 outliers final: 55 residues processed: 611 average time/residue: 0.2667 time to fit residues: 257.4709 Evaluate side-chains 538 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 471 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 443 HIS Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 665 PHE Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 0.4980 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19924 Z= 0.181 Angle : 0.569 13.528 26964 Z= 0.285 Chirality : 0.040 0.146 3108 Planarity : 0.003 0.030 3324 Dihedral : 4.041 15.833 2656 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.84 % Allowed : 18.55 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.82 (0.17), residues: 2400 helix: 0.18 (0.13), residues: 1388 sheet: -1.98 (0.49), residues: 84 loop : -1.42 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.004 0.001 HIS A 298 PHE 0.016 0.001 PHE C 665 TYR 0.019 0.001 TYR D 299 ARG 0.006 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 501 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8002 (p) cc_final: 0.7666 (t) REVERT: A 283 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 301 THR cc_start: 0.8822 (p) cc_final: 0.8577 (p) REVERT: A 367 MET cc_start: 0.7244 (mmm) cc_final: 0.6428 (mmm) REVERT: A 449 GLU cc_start: 0.7769 (tp30) cc_final: 0.7560 (tp30) REVERT: A 507 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 520 PHE cc_start: 0.8871 (t80) cc_final: 0.8640 (t80) REVERT: A 553 SER cc_start: 0.9461 (m) cc_final: 0.9157 (p) REVERT: A 609 ASP cc_start: 0.7530 (m-30) cc_final: 0.7100 (t0) REVERT: A 614 LEU cc_start: 0.9207 (tp) cc_final: 0.8956 (tp) REVERT: A 615 LEU cc_start: 0.9028 (mt) cc_final: 0.8773 (tp) REVERT: A 665 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8535 (t80) REVERT: A 694 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8942 (mm) REVERT: A 703 PHE cc_start: 0.8879 (t80) cc_final: 0.8525 (t80) REVERT: A 727 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: A 750 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8002 (mmtt) REVERT: B 154 VAL cc_start: 0.9316 (m) cc_final: 0.9051 (p) REVERT: B 181 PHE cc_start: 0.7572 (m-80) cc_final: 0.7348 (m-80) REVERT: B 186 THR cc_start: 0.8037 (p) cc_final: 0.7676 (t) REVERT: B 283 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8898 (mm) REVERT: B 367 MET cc_start: 0.7344 (mmm) cc_final: 0.6660 (mmm) REVERT: B 520 PHE cc_start: 0.8905 (t80) cc_final: 0.8681 (t80) REVERT: B 553 SER cc_start: 0.9550 (m) cc_final: 0.9190 (p) REVERT: B 609 ASP cc_start: 0.7761 (m-30) cc_final: 0.7403 (t0) REVERT: B 615 LEU cc_start: 0.9192 (tp) cc_final: 0.8901 (tp) REVERT: B 665 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8520 (t80) REVERT: B 672 LEU cc_start: 0.9289 (mt) cc_final: 0.9076 (mm) REVERT: B 694 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 727 GLN cc_start: 0.7017 (pt0) cc_final: 0.6594 (pm20) REVERT: C 154 VAL cc_start: 0.9390 (m) cc_final: 0.9138 (p) REVERT: C 186 THR cc_start: 0.7884 (p) cc_final: 0.7516 (t) REVERT: C 222 PHE cc_start: 0.7330 (t80) cc_final: 0.7097 (t80) REVERT: C 263 GLN cc_start: 0.7678 (mt0) cc_final: 0.7266 (mt0) REVERT: C 283 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8844 (mm) REVERT: C 383 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8355 (tp40) REVERT: C 449 GLU cc_start: 0.7938 (tp30) cc_final: 0.7726 (tp30) REVERT: C 483 LEU cc_start: 0.9231 (mp) cc_final: 0.9020 (mp) REVERT: C 520 PHE cc_start: 0.9127 (t80) cc_final: 0.8680 (t80) REVERT: C 553 SER cc_start: 0.9712 (m) cc_final: 0.9219 (p) REVERT: C 571 LEU cc_start: 0.9215 (tt) cc_final: 0.8987 (tt) REVERT: C 584 ASN cc_start: 0.8702 (m110) cc_final: 0.8084 (m110) REVERT: C 609 ASP cc_start: 0.7733 (m-30) cc_final: 0.7161 (t0) REVERT: C 615 LEU cc_start: 0.9182 (mt) cc_final: 0.8917 (tp) REVERT: C 698 TYR cc_start: 0.8628 (t80) cc_final: 0.8202 (t80) REVERT: C 703 PHE cc_start: 0.8913 (t80) cc_final: 0.8563 (t80) REVERT: C 706 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8456 (tp) REVERT: C 709 MET cc_start: 0.8647 (mmt) cc_final: 0.8231 (mmt) REVERT: C 739 ASP cc_start: 0.7656 (t0) cc_final: 0.7372 (t0) REVERT: D 151 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7719 (t80) REVERT: D 154 VAL cc_start: 0.9351 (m) cc_final: 0.9083 (p) REVERT: D 181 PHE cc_start: 0.7905 (m-80) cc_final: 0.7639 (m-80) REVERT: D 186 THR cc_start: 0.7741 (p) cc_final: 0.7362 (t) REVERT: D 283 LEU cc_start: 0.9150 (mm) cc_final: 0.8717 (mm) REVERT: D 387 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7731 (mtm-85) REVERT: D 449 GLU cc_start: 0.8093 (tp30) cc_final: 0.7769 (tp30) REVERT: D 453 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7794 (mm-30) REVERT: D 520 PHE cc_start: 0.8968 (t80) cc_final: 0.8638 (t80) REVERT: D 553 SER cc_start: 0.9606 (m) cc_final: 0.9276 (p) REVERT: D 609 ASP cc_start: 0.8126 (m-30) cc_final: 0.7588 (t0) REVERT: D 615 LEU cc_start: 0.8995 (mt) cc_final: 0.8778 (tp) REVERT: D 698 TYR cc_start: 0.8504 (t80) cc_final: 0.8252 (t80) REVERT: D 700 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8789 (tt) REVERT: D 703 PHE cc_start: 0.8907 (t80) cc_final: 0.8618 (t80) REVERT: D 727 GLN cc_start: 0.7119 (pt0) cc_final: 0.6751 (pm20) outliers start: 102 outliers final: 65 residues processed: 570 average time/residue: 0.2670 time to fit residues: 243.4320 Evaluate side-chains 553 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 475 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 665 PHE Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 GLN B 218 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 GLN D 218 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19924 Z= 0.331 Angle : 0.673 11.402 26964 Z= 0.343 Chirality : 0.043 0.158 3108 Planarity : 0.004 0.029 3324 Dihedral : 4.465 18.393 2656 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 7.21 % Allowed : 16.98 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.62 (0.17), residues: 2400 helix: 0.38 (0.13), residues: 1400 sheet: -2.30 (0.46), residues: 88 loop : -1.38 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 459 HIS 0.007 0.001 HIS A 443 PHE 0.018 0.002 PHE A 181 TYR 0.017 0.002 TYR D 563 ARG 0.007 0.001 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 463 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8213 (p) cc_final: 0.7822 (t) REVERT: A 267 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8608 (tpp80) REVERT: A 367 MET cc_start: 0.7599 (mmm) cc_final: 0.7355 (mmm) REVERT: A 375 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (mttp) REVERT: A 503 ASP cc_start: 0.7942 (m-30) cc_final: 0.7589 (m-30) REVERT: A 504 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 507 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8250 (mt) REVERT: A 520 PHE cc_start: 0.9004 (t80) cc_final: 0.8714 (t80) REVERT: A 541 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 553 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9227 (p) REVERT: A 571 LEU cc_start: 0.9311 (tp) cc_final: 0.9077 (tt) REVERT: A 609 ASP cc_start: 0.7651 (m-30) cc_final: 0.7290 (t0) REVERT: A 615 LEU cc_start: 0.9180 (mt) cc_final: 0.8898 (tp) REVERT: A 621 MET cc_start: 0.8880 (mmt) cc_final: 0.8624 (mmp) REVERT: A 628 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 669 LEU cc_start: 0.9268 (tp) cc_final: 0.9043 (tp) REVERT: A 726 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7393 (mmmm) REVERT: A 727 GLN cc_start: 0.7440 (pt0) cc_final: 0.7002 (pm20) REVERT: B 154 VAL cc_start: 0.9369 (m) cc_final: 0.9137 (p) REVERT: B 186 THR cc_start: 0.8147 (p) cc_final: 0.7722 (t) REVERT: B 263 GLN cc_start: 0.7746 (mt0) cc_final: 0.7455 (mt0) REVERT: B 267 ARG cc_start: 0.9012 (mtp-110) cc_final: 0.8689 (tpp80) REVERT: B 367 MET cc_start: 0.7780 (mmm) cc_final: 0.7560 (mmm) REVERT: B 431 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7167 (mm-30) REVERT: B 478 MET cc_start: 0.8354 (tpp) cc_final: 0.8129 (tpp) REVERT: B 520 PHE cc_start: 0.9017 (t80) cc_final: 0.8755 (t80) REVERT: B 541 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8114 (mm) REVERT: B 553 SER cc_start: 0.9682 (OUTLIER) cc_final: 0.9341 (p) REVERT: B 609 ASP cc_start: 0.7815 (m-30) cc_final: 0.7439 (t0) REVERT: B 621 MET cc_start: 0.8952 (mmp) cc_final: 0.8575 (mmt) REVERT: B 628 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8667 (mm) REVERT: B 726 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7422 (mmmm) REVERT: C 186 THR cc_start: 0.8114 (p) cc_final: 0.7721 (t) REVERT: C 263 GLN cc_start: 0.7800 (mt0) cc_final: 0.7335 (mt0) REVERT: C 283 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 431 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7376 (mm-30) REVERT: C 449 GLU cc_start: 0.8094 (tp30) cc_final: 0.7842 (tp30) REVERT: C 483 LEU cc_start: 0.9215 (mp) cc_final: 0.8999 (mp) REVERT: C 520 PHE cc_start: 0.9193 (t80) cc_final: 0.8691 (t80) REVERT: C 553 SER cc_start: 0.9706 (m) cc_final: 0.9320 (p) REVERT: C 571 LEU cc_start: 0.9350 (tt) cc_final: 0.9123 (tt) REVERT: C 584 ASN cc_start: 0.8755 (m110) cc_final: 0.8136 (m110) REVERT: C 609 ASP cc_start: 0.7854 (m-30) cc_final: 0.7506 (t0) REVERT: C 615 LEU cc_start: 0.9268 (mt) cc_final: 0.9042 (tp) REVERT: C 668 ASP cc_start: 0.8091 (m-30) cc_final: 0.7756 (m-30) REVERT: C 697 THR cc_start: 0.9016 (p) cc_final: 0.8774 (m) REVERT: C 698 TYR cc_start: 0.8637 (t80) cc_final: 0.8361 (t80) REVERT: C 709 MET cc_start: 0.8714 (mmt) cc_final: 0.8507 (mmt) REVERT: C 739 ASP cc_start: 0.7492 (t0) cc_final: 0.7265 (t0) REVERT: D 151 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7903 (t80) REVERT: D 186 THR cc_start: 0.7941 (p) cc_final: 0.7510 (t) REVERT: D 222 PHE cc_start: 0.7524 (t80) cc_final: 0.7170 (t80) REVERT: D 263 GLN cc_start: 0.8069 (mt0) cc_final: 0.7659 (mm-40) REVERT: D 283 LEU cc_start: 0.9073 (mm) cc_final: 0.8768 (mm) REVERT: D 453 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7925 (mm-30) REVERT: D 478 MET cc_start: 0.8534 (tpp) cc_final: 0.8104 (tpp) REVERT: D 520 PHE cc_start: 0.9072 (t80) cc_final: 0.8726 (t80) REVERT: D 541 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7748 (mm) REVERT: D 553 SER cc_start: 0.9740 (m) cc_final: 0.9359 (p) REVERT: D 609 ASP cc_start: 0.8014 (m-30) cc_final: 0.7518 (t0) REVERT: D 615 LEU cc_start: 0.9038 (mt) cc_final: 0.8820 (tp) REVERT: D 631 LEU cc_start: 0.9210 (mp) cc_final: 0.8864 (mp) REVERT: D 700 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8765 (tt) REVERT: D 709 MET cc_start: 0.8735 (mmp) cc_final: 0.8472 (mmt) REVERT: D 726 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7478 (mmmm) REVERT: D 727 GLN cc_start: 0.7479 (pt0) cc_final: 0.7074 (pm20) outliers start: 152 outliers final: 98 residues processed: 560 average time/residue: 0.2649 time to fit residues: 237.8075 Evaluate side-chains 541 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 430 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 665 PHE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.0470 chunk 76 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19924 Z= 0.270 Angle : 0.623 11.739 26964 Z= 0.316 Chirality : 0.042 0.273 3108 Planarity : 0.003 0.029 3324 Dihedral : 4.356 18.062 2656 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.50 % Allowed : 18.88 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.33 (0.17), residues: 2400 helix: 0.61 (0.14), residues: 1388 sheet: -2.20 (0.46), residues: 88 loop : -1.22 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 459 HIS 0.006 0.001 HIS A 443 PHE 0.013 0.002 PHE A 222 TYR 0.021 0.001 TYR A 563 ARG 0.006 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 455 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8213 (p) cc_final: 0.7826 (t) REVERT: A 267 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8597 (tpp80) REVERT: A 503 ASP cc_start: 0.7987 (m-30) cc_final: 0.7653 (m-30) REVERT: A 504 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: A 507 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 520 PHE cc_start: 0.8998 (t80) cc_final: 0.8722 (t80) REVERT: A 541 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8242 (mm) REVERT: A 553 SER cc_start: 0.9528 (OUTLIER) cc_final: 0.9245 (p) REVERT: A 609 ASP cc_start: 0.7597 (m-30) cc_final: 0.7134 (t0) REVERT: A 615 LEU cc_start: 0.9251 (mt) cc_final: 0.8975 (tp) REVERT: A 621 MET cc_start: 0.8870 (mmt) cc_final: 0.8636 (mmp) REVERT: A 726 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7429 (mmmm) REVERT: A 727 GLN cc_start: 0.7322 (pt0) cc_final: 0.6949 (pm20) REVERT: A 739 ASP cc_start: 0.7652 (t0) cc_final: 0.7435 (t0) REVERT: B 154 VAL cc_start: 0.9356 (m) cc_final: 0.9110 (p) REVERT: B 186 THR cc_start: 0.8150 (p) cc_final: 0.7758 (t) REVERT: B 222 PHE cc_start: 0.7453 (t80) cc_final: 0.7242 (t80) REVERT: B 267 ARG cc_start: 0.8959 (mtp-110) cc_final: 0.8684 (tpp80) REVERT: B 283 LEU cc_start: 0.9038 (mm) cc_final: 0.8778 (mm) REVERT: B 431 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7174 (mm-30) REVERT: B 520 PHE cc_start: 0.8987 (t80) cc_final: 0.8689 (t80) REVERT: B 541 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8147 (mm) REVERT: B 553 SER cc_start: 0.9621 (m) cc_final: 0.9303 (p) REVERT: B 609 ASP cc_start: 0.7774 (m-30) cc_final: 0.7257 (t0) REVERT: B 709 MET cc_start: 0.8684 (mmt) cc_final: 0.8447 (mmt) REVERT: B 726 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7437 (mmmm) REVERT: B 739 ASP cc_start: 0.7821 (t0) cc_final: 0.7584 (t0) REVERT: C 186 THR cc_start: 0.8151 (p) cc_final: 0.7777 (t) REVERT: C 263 GLN cc_start: 0.7761 (mt0) cc_final: 0.7287 (mt0) REVERT: C 283 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8798 (mm) REVERT: C 383 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (tp40) REVERT: C 431 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7462 (mm-30) REVERT: C 449 GLU cc_start: 0.8172 (tp30) cc_final: 0.7811 (tp30) REVERT: C 453 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7931 (mm-30) REVERT: C 483 LEU cc_start: 0.9161 (mp) cc_final: 0.8942 (mp) REVERT: C 510 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8042 (tt0) REVERT: C 520 PHE cc_start: 0.9159 (t80) cc_final: 0.8696 (t80) REVERT: C 553 SER cc_start: 0.9728 (m) cc_final: 0.9314 (p) REVERT: C 571 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9068 (tt) REVERT: C 609 ASP cc_start: 0.7807 (m-30) cc_final: 0.7438 (t0) REVERT: C 615 LEU cc_start: 0.9253 (mt) cc_final: 0.8985 (tp) REVERT: D 151 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7857 (t80) REVERT: D 186 THR cc_start: 0.7942 (p) cc_final: 0.7555 (t) REVERT: D 283 LEU cc_start: 0.9147 (mm) cc_final: 0.8842 (mm) REVERT: D 367 MET cc_start: 0.8276 (mmm) cc_final: 0.7724 (mmm) REVERT: D 431 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7365 (mm-30) REVERT: D 449 GLU cc_start: 0.8102 (tp30) cc_final: 0.7868 (tp30) REVERT: D 453 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7912 (mm-30) REVERT: D 520 PHE cc_start: 0.9074 (t80) cc_final: 0.8710 (t80) REVERT: D 541 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7779 (mm) REVERT: D 553 SER cc_start: 0.9643 (OUTLIER) cc_final: 0.9348 (p) REVERT: D 609 ASP cc_start: 0.7992 (m-30) cc_final: 0.7481 (t0) REVERT: D 631 LEU cc_start: 0.9221 (mp) cc_final: 0.8871 (mp) REVERT: D 694 LEU cc_start: 0.9434 (mm) cc_final: 0.9201 (mm) REVERT: D 700 ILE cc_start: 0.9129 (tp) cc_final: 0.8770 (tt) REVERT: D 709 MET cc_start: 0.8617 (mmp) cc_final: 0.8402 (mmt) REVERT: D 726 LYS cc_start: 0.7774 (mmtm) cc_final: 0.7478 (mmmm) outliers start: 137 outliers final: 94 residues processed: 546 average time/residue: 0.2625 time to fit residues: 229.7983 Evaluate side-chains 522 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 417 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 665 PHE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19924 Z= 0.193 Angle : 0.601 12.436 26964 Z= 0.298 Chirality : 0.041 0.321 3108 Planarity : 0.003 0.027 3324 Dihedral : 4.143 16.760 2656 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.50 % Allowed : 20.87 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.07 (0.17), residues: 2400 helix: 0.79 (0.14), residues: 1408 sheet: -2.00 (0.46), residues: 88 loop : -1.11 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 459 HIS 0.005 0.001 HIS A 443 PHE 0.039 0.001 PHE B 165 TYR 0.020 0.001 TYR A 563 ARG 0.004 0.000 ARG D 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 461 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8162 (p) cc_final: 0.7786 (t) REVERT: A 267 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8547 (tpp80) REVERT: A 503 ASP cc_start: 0.7979 (m-30) cc_final: 0.7645 (m-30) REVERT: A 504 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: A 507 LEU cc_start: 0.8767 (mt) cc_final: 0.8305 (mt) REVERT: A 520 PHE cc_start: 0.8979 (t80) cc_final: 0.8711 (t80) REVERT: A 541 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 553 SER cc_start: 0.9436 (m) cc_final: 0.9213 (p) REVERT: A 609 ASP cc_start: 0.7595 (m-30) cc_final: 0.7259 (t0) REVERT: A 615 LEU cc_start: 0.9192 (mt) cc_final: 0.8894 (tp) REVERT: A 698 TYR cc_start: 0.8531 (t80) cc_final: 0.8310 (t80) REVERT: A 726 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7441 (mmmm) REVERT: A 739 ASP cc_start: 0.7631 (t0) cc_final: 0.7402 (t0) REVERT: B 154 VAL cc_start: 0.9352 (m) cc_final: 0.9099 (p) REVERT: B 186 THR cc_start: 0.8092 (p) cc_final: 0.7724 (t) REVERT: B 267 ARG cc_start: 0.8953 (mtp-110) cc_final: 0.8679 (tpp80) REVERT: B 283 LEU cc_start: 0.9013 (mm) cc_final: 0.8744 (mm) REVERT: B 449 GLU cc_start: 0.7780 (tp30) cc_final: 0.7476 (tp30) REVERT: B 520 PHE cc_start: 0.8940 (t80) cc_final: 0.8619 (t80) REVERT: B 553 SER cc_start: 0.9546 (m) cc_final: 0.9295 (p) REVERT: B 558 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 609 ASP cc_start: 0.7642 (m-30) cc_final: 0.7238 (t0) REVERT: B 628 LEU cc_start: 0.9153 (mm) cc_final: 0.8881 (mp) REVERT: B 672 LEU cc_start: 0.9238 (mt) cc_final: 0.8984 (mm) REVERT: B 726 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7430 (mmmm) REVERT: B 739 ASP cc_start: 0.7802 (t0) cc_final: 0.7583 (t0) REVERT: B 742 ARG cc_start: 0.8677 (mmt90) cc_final: 0.8087 (mmm-85) REVERT: C 186 THR cc_start: 0.8107 (p) cc_final: 0.7751 (t) REVERT: C 263 GLN cc_start: 0.7792 (mt0) cc_final: 0.7348 (mt0) REVERT: C 283 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8818 (mm) REVERT: C 431 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7399 (mm-30) REVERT: C 449 GLU cc_start: 0.8085 (tp30) cc_final: 0.7628 (tp30) REVERT: C 453 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7672 (mm-30) REVERT: C 483 LEU cc_start: 0.9126 (mp) cc_final: 0.8917 (mp) REVERT: C 503 ASP cc_start: 0.7902 (m-30) cc_final: 0.7498 (m-30) REVERT: C 520 PHE cc_start: 0.9143 (t80) cc_final: 0.8676 (t80) REVERT: C 553 SER cc_start: 0.9704 (m) cc_final: 0.9313 (p) REVERT: C 571 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9005 (tt) REVERT: C 584 ASN cc_start: 0.9121 (m-40) cc_final: 0.8824 (m110) REVERT: C 609 ASP cc_start: 0.7815 (m-30) cc_final: 0.7366 (t0) REVERT: C 615 LEU cc_start: 0.9190 (mt) cc_final: 0.8950 (tp) REVERT: D 151 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7848 (t80) REVERT: D 186 THR cc_start: 0.7970 (p) cc_final: 0.7600 (t) REVERT: D 283 LEU cc_start: 0.9145 (mm) cc_final: 0.8877 (mm) REVERT: D 367 MET cc_start: 0.8048 (mmm) cc_final: 0.7571 (mmm) REVERT: D 431 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7233 (mm-30) REVERT: D 449 GLU cc_start: 0.8001 (tp30) cc_final: 0.7755 (tp30) REVERT: D 453 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7880 (mm-30) REVERT: D 478 MET cc_start: 0.8182 (tpp) cc_final: 0.7763 (tpp) REVERT: D 503 ASP cc_start: 0.7947 (m-30) cc_final: 0.7574 (m-30) REVERT: D 520 PHE cc_start: 0.9011 (t80) cc_final: 0.8570 (t80) REVERT: D 541 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7708 (mm) REVERT: D 553 SER cc_start: 0.9615 (OUTLIER) cc_final: 0.9307 (p) REVERT: D 609 ASP cc_start: 0.7974 (m-30) cc_final: 0.7432 (t0) REVERT: D 631 LEU cc_start: 0.9201 (mp) cc_final: 0.8847 (mp) REVERT: D 694 LEU cc_start: 0.9429 (mm) cc_final: 0.9156 (mm) REVERT: D 700 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8752 (tt) REVERT: D 703 PHE cc_start: 0.9004 (t80) cc_final: 0.8658 (t80) REVERT: D 726 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7475 (mmmm) REVERT: D 727 GLN cc_start: 0.7403 (pt0) cc_final: 0.7175 (pt0) outliers start: 116 outliers final: 85 residues processed: 544 average time/residue: 0.2506 time to fit residues: 220.5015 Evaluate side-chains 526 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 432 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS B 363 ASN ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19924 Z= 0.204 Angle : 0.618 13.957 26964 Z= 0.303 Chirality : 0.042 0.342 3108 Planarity : 0.003 0.026 3324 Dihedral : 4.086 16.479 2656 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.60 % Allowed : 21.49 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.01 (0.17), residues: 2400 helix: 0.87 (0.14), residues: 1404 sheet: -1.94 (0.45), residues: 88 loop : -1.09 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 459 HIS 0.005 0.001 HIS A 443 PHE 0.030 0.001 PHE B 165 TYR 0.020 0.001 TYR A 563 ARG 0.004 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 450 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8119 (p) cc_final: 0.7744 (t) REVERT: A 267 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8542 (tpp80) REVERT: A 367 MET cc_start: 0.8163 (mmm) cc_final: 0.7945 (mmm) REVERT: A 503 ASP cc_start: 0.7999 (m-30) cc_final: 0.7687 (m-30) REVERT: A 504 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: A 507 LEU cc_start: 0.8785 (mt) cc_final: 0.8321 (mt) REVERT: A 520 PHE cc_start: 0.8937 (t80) cc_final: 0.8684 (t80) REVERT: A 541 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 553 SER cc_start: 0.9451 (m) cc_final: 0.9234 (p) REVERT: A 609 ASP cc_start: 0.7674 (m-30) cc_final: 0.7390 (t0) REVERT: A 615 LEU cc_start: 0.9213 (mt) cc_final: 0.8939 (tp) REVERT: A 727 GLN cc_start: 0.7100 (pt0) cc_final: 0.6881 (pm20) REVERT: B 154 VAL cc_start: 0.9356 (m) cc_final: 0.9101 (p) REVERT: B 186 THR cc_start: 0.8043 (p) cc_final: 0.7624 (t) REVERT: B 267 ARG cc_start: 0.8956 (mtp-110) cc_final: 0.8680 (tpp80) REVERT: B 283 LEU cc_start: 0.9088 (mm) cc_final: 0.8872 (mm) REVERT: B 503 ASP cc_start: 0.7975 (m-30) cc_final: 0.7617 (m-30) REVERT: B 504 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: B 520 PHE cc_start: 0.8939 (t80) cc_final: 0.8644 (t80) REVERT: B 553 SER cc_start: 0.9560 (m) cc_final: 0.9282 (p) REVERT: B 558 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9336 (mm) REVERT: B 573 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9206 (t) REVERT: B 609 ASP cc_start: 0.7629 (m-30) cc_final: 0.7163 (t0) REVERT: B 615 LEU cc_start: 0.9193 (tp) cc_final: 0.8983 (tt) REVERT: B 628 LEU cc_start: 0.9161 (mm) cc_final: 0.8873 (mp) REVERT: B 726 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7421 (mmmm) REVERT: B 739 ASP cc_start: 0.7787 (t0) cc_final: 0.7571 (t0) REVERT: C 186 THR cc_start: 0.8036 (p) cc_final: 0.7636 (t) REVERT: C 263 GLN cc_start: 0.7776 (mt0) cc_final: 0.7332 (mt0) REVERT: C 283 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8827 (mm) REVERT: C 449 GLU cc_start: 0.8021 (tp30) cc_final: 0.7531 (tp30) REVERT: C 453 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7730 (mm-30) REVERT: C 503 ASP cc_start: 0.7918 (m-30) cc_final: 0.7465 (m-30) REVERT: C 520 PHE cc_start: 0.9133 (t80) cc_final: 0.8691 (t80) REVERT: C 553 SER cc_start: 0.9694 (m) cc_final: 0.9296 (p) REVERT: C 571 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9016 (tt) REVERT: C 584 ASN cc_start: 0.9102 (m-40) cc_final: 0.8825 (m110) REVERT: C 609 ASP cc_start: 0.7850 (m-30) cc_final: 0.7595 (t0) REVERT: C 615 LEU cc_start: 0.9209 (mt) cc_final: 0.8855 (tp) REVERT: C 742 ARG cc_start: 0.8787 (mmt90) cc_final: 0.8517 (mmm-85) REVERT: D 151 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7724 (t80) REVERT: D 186 THR cc_start: 0.7973 (p) cc_final: 0.7603 (t) REVERT: D 222 PHE cc_start: 0.7701 (t80) cc_final: 0.7390 (t80) REVERT: D 283 LEU cc_start: 0.9132 (mm) cc_final: 0.8875 (mm) REVERT: D 367 MET cc_start: 0.7962 (mmm) cc_final: 0.7551 (mmm) REVERT: D 431 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7396 (mm-30) REVERT: D 449 GLU cc_start: 0.7992 (tp30) cc_final: 0.7730 (tp30) REVERT: D 453 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7893 (mm-30) REVERT: D 478 MET cc_start: 0.8264 (tpp) cc_final: 0.7915 (tpp) REVERT: D 503 ASP cc_start: 0.8016 (m-30) cc_final: 0.7675 (m-30) REVERT: D 520 PHE cc_start: 0.8991 (t80) cc_final: 0.8563 (t80) REVERT: D 541 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7776 (mm) REVERT: D 553 SER cc_start: 0.9631 (OUTLIER) cc_final: 0.9319 (p) REVERT: D 573 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9225 (t) REVERT: D 609 ASP cc_start: 0.8004 (m-30) cc_final: 0.7533 (t0) REVERT: D 631 LEU cc_start: 0.9194 (mp) cc_final: 0.8843 (mp) REVERT: D 694 LEU cc_start: 0.9420 (mm) cc_final: 0.9192 (mm) REVERT: D 700 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8688 (tt) REVERT: D 703 PHE cc_start: 0.8998 (t80) cc_final: 0.8653 (t80) REVERT: D 726 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7470 (mmmm) outliers start: 118 outliers final: 88 residues processed: 525 average time/residue: 0.2619 time to fit residues: 222.5990 Evaluate side-chains 535 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 435 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 670 PHE Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 0.1980 chunk 215 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 HIS D 727 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19924 Z= 0.165 Angle : 0.615 13.917 26964 Z= 0.295 Chirality : 0.041 0.333 3108 Planarity : 0.003 0.027 3324 Dihedral : 3.960 21.953 2656 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.70 % Allowed : 22.87 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.22 (0.18), residues: 2400 helix: 1.02 (0.14), residues: 1396 sheet: -1.79 (0.44), residues: 88 loop : -0.95 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 459 HIS 0.005 0.001 HIS A 443 PHE 0.028 0.001 PHE B 165 TYR 0.021 0.001 TYR A 563 ARG 0.003 0.000 ARG D 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 476 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8019 (p) cc_final: 0.7639 (t) REVERT: A 267 ARG cc_start: 0.8802 (mtp-110) cc_final: 0.8553 (tpp80) REVERT: A 503 ASP cc_start: 0.7936 (m-30) cc_final: 0.7611 (m-30) REVERT: A 504 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: A 507 LEU cc_start: 0.8847 (mt) cc_final: 0.8421 (mt) REVERT: A 520 PHE cc_start: 0.8918 (t80) cc_final: 0.8610 (t80) REVERT: A 541 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8181 (mm) REVERT: A 553 SER cc_start: 0.9438 (m) cc_final: 0.9205 (p) REVERT: A 609 ASP cc_start: 0.7610 (m-30) cc_final: 0.7314 (t0) REVERT: A 615 LEU cc_start: 0.9174 (mt) cc_final: 0.8924 (tp) REVERT: A 703 PHE cc_start: 0.8874 (t80) cc_final: 0.8563 (t80) REVERT: A 716 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7053 (pt0) REVERT: A 727 GLN cc_start: 0.6966 (pt0) cc_final: 0.6751 (pm20) REVERT: B 151 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 186 THR cc_start: 0.8018 (p) cc_final: 0.7640 (t) REVERT: B 267 ARG cc_start: 0.8950 (mtp-110) cc_final: 0.8688 (tpp80) REVERT: B 283 LEU cc_start: 0.9090 (mm) cc_final: 0.8878 (mm) REVERT: B 449 GLU cc_start: 0.7574 (tp30) cc_final: 0.7325 (tp30) REVERT: B 503 ASP cc_start: 0.7958 (m-30) cc_final: 0.7603 (m-30) REVERT: B 504 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 520 PHE cc_start: 0.8915 (t80) cc_final: 0.8616 (t80) REVERT: B 553 SER cc_start: 0.9538 (m) cc_final: 0.9273 (p) REVERT: B 609 ASP cc_start: 0.7670 (m-30) cc_final: 0.7334 (t0) REVERT: B 672 LEU cc_start: 0.9213 (mt) cc_final: 0.8948 (mm) REVERT: B 680 GLU cc_start: 0.7476 (mp0) cc_final: 0.7269 (mp0) REVERT: B 703 PHE cc_start: 0.8921 (t80) cc_final: 0.8613 (t80) REVERT: B 716 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7311 (mt-10) REVERT: B 726 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7486 (mmmm) REVERT: C 186 THR cc_start: 0.7988 (p) cc_final: 0.7630 (t) REVERT: C 283 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 449 GLU cc_start: 0.7963 (tp30) cc_final: 0.7445 (tp30) REVERT: C 453 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7690 (mm-30) REVERT: C 490 MET cc_start: 0.7541 (mtm) cc_final: 0.7219 (mpp) REVERT: C 503 ASP cc_start: 0.7939 (m-30) cc_final: 0.7516 (m-30) REVERT: C 504 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: C 520 PHE cc_start: 0.9116 (t80) cc_final: 0.8640 (t80) REVERT: C 553 SER cc_start: 0.9593 (m) cc_final: 0.9227 (p) REVERT: C 571 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8960 (tt) REVERT: C 609 ASP cc_start: 0.7806 (m-30) cc_final: 0.7513 (t0) REVERT: C 615 LEU cc_start: 0.9161 (mt) cc_final: 0.8827 (tp) REVERT: C 739 ASP cc_start: 0.7685 (t0) cc_final: 0.7331 (t0) REVERT: D 151 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7695 (t80) REVERT: D 186 THR cc_start: 0.7848 (p) cc_final: 0.7453 (t) REVERT: D 222 PHE cc_start: 0.7723 (t80) cc_final: 0.7404 (t80) REVERT: D 283 LEU cc_start: 0.9104 (mm) cc_final: 0.8755 (mm) REVERT: D 449 GLU cc_start: 0.7899 (tp30) cc_final: 0.7513 (tp30) REVERT: D 453 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7878 (mm-30) REVERT: D 503 ASP cc_start: 0.8073 (m-30) cc_final: 0.7759 (m-30) REVERT: D 504 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: D 507 LEU cc_start: 0.9253 (tp) cc_final: 0.8761 (mt) REVERT: D 510 GLU cc_start: 0.8429 (tt0) cc_final: 0.8228 (tt0) REVERT: D 520 PHE cc_start: 0.8937 (t80) cc_final: 0.8509 (t80) REVERT: D 541 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7735 (mm) REVERT: D 553 SER cc_start: 0.9611 (m) cc_final: 0.9280 (p) REVERT: D 609 ASP cc_start: 0.7948 (m-30) cc_final: 0.7641 (t0) REVERT: D 631 LEU cc_start: 0.9188 (mp) cc_final: 0.8850 (mp) REVERT: D 694 LEU cc_start: 0.9436 (mm) cc_final: 0.9214 (mm) REVERT: D 700 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8660 (tt) REVERT: D 703 PHE cc_start: 0.8961 (t80) cc_final: 0.8631 (t80) REVERT: D 726 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7467 (mmmm) REVERT: D 742 ARG cc_start: 0.8701 (mmt90) cc_final: 0.8252 (mmm-85) outliers start: 99 outliers final: 70 residues processed: 541 average time/residue: 0.2676 time to fit residues: 232.6839 Evaluate side-chains 533 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 452 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 670 PHE Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0270 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19924 Z= 0.172 Angle : 0.635 14.172 26964 Z= 0.304 Chirality : 0.041 0.324 3108 Planarity : 0.003 0.025 3324 Dihedral : 3.918 19.115 2656 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.03 % Allowed : 24.15 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.24 (0.17), residues: 2400 helix: 1.02 (0.14), residues: 1396 sheet: -1.75 (0.44), residues: 88 loop : -0.93 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 459 HIS 0.004 0.001 HIS A 443 PHE 0.026 0.001 PHE B 165 TYR 0.020 0.001 TYR D 563 ARG 0.004 0.000 ARG C 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 466 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.7992 (p) cc_final: 0.7617 (t) REVERT: A 267 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8552 (tpp80) REVERT: A 503 ASP cc_start: 0.7970 (m-30) cc_final: 0.7736 (m-30) REVERT: A 504 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: A 507 LEU cc_start: 0.8854 (mt) cc_final: 0.8415 (mt) REVERT: A 520 PHE cc_start: 0.8910 (t80) cc_final: 0.8585 (t80) REVERT: A 541 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 553 SER cc_start: 0.9444 (m) cc_final: 0.9179 (p) REVERT: A 609 ASP cc_start: 0.7598 (m-30) cc_final: 0.7356 (t0) REVERT: A 615 LEU cc_start: 0.9127 (mt) cc_final: 0.8881 (tp) REVERT: A 716 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7121 (pt0) REVERT: A 727 GLN cc_start: 0.6859 (pt0) cc_final: 0.6655 (pm20) REVERT: B 186 THR cc_start: 0.7938 (p) cc_final: 0.7565 (t) REVERT: B 267 ARG cc_start: 0.8948 (mtp-110) cc_final: 0.8682 (tpp80) REVERT: B 283 LEU cc_start: 0.9093 (mm) cc_final: 0.8824 (mm) REVERT: B 431 GLU cc_start: 0.7707 (tp30) cc_final: 0.7479 (tp30) REVERT: B 449 GLU cc_start: 0.7516 (tp30) cc_final: 0.7252 (tp30) REVERT: B 503 ASP cc_start: 0.7971 (m-30) cc_final: 0.7716 (m-30) REVERT: B 504 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 520 PHE cc_start: 0.8921 (t80) cc_final: 0.8570 (t80) REVERT: B 553 SER cc_start: 0.9622 (m) cc_final: 0.9273 (p) REVERT: B 609 ASP cc_start: 0.7650 (m-30) cc_final: 0.7337 (t0) REVERT: B 672 LEU cc_start: 0.9204 (mt) cc_final: 0.8933 (mm) REVERT: B 680 GLU cc_start: 0.7455 (mp0) cc_final: 0.7240 (mp0) REVERT: B 694 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9307 (mm) REVERT: B 703 PHE cc_start: 0.8922 (t80) cc_final: 0.8575 (t80) REVERT: B 716 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 726 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7481 (mmmm) REVERT: C 186 THR cc_start: 0.7968 (p) cc_final: 0.7624 (t) REVERT: C 283 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 449 GLU cc_start: 0.7964 (tp30) cc_final: 0.7686 (tp30) REVERT: C 453 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7803 (mm-30) REVERT: C 490 MET cc_start: 0.7532 (mtm) cc_final: 0.7208 (mpp) REVERT: C 503 ASP cc_start: 0.7958 (m-30) cc_final: 0.7559 (m-30) REVERT: C 504 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: C 520 PHE cc_start: 0.9115 (t80) cc_final: 0.8674 (t80) REVERT: C 553 SER cc_start: 0.9554 (m) cc_final: 0.9205 (p) REVERT: C 571 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8947 (tt) REVERT: C 609 ASP cc_start: 0.7800 (m-30) cc_final: 0.7573 (t0) REVERT: C 615 LEU cc_start: 0.9194 (mt) cc_final: 0.8895 (tp) REVERT: C 631 LEU cc_start: 0.9019 (mt) cc_final: 0.8779 (tt) REVERT: C 739 ASP cc_start: 0.7687 (t0) cc_final: 0.7339 (t0) REVERT: D 151 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7665 (t80) REVERT: D 186 THR cc_start: 0.7790 (p) cc_final: 0.7421 (t) REVERT: D 283 LEU cc_start: 0.9152 (mm) cc_final: 0.8793 (mm) REVERT: D 431 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7394 (tp30) REVERT: D 449 GLU cc_start: 0.7863 (tp30) cc_final: 0.6847 (tp30) REVERT: D 453 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7872 (mp0) REVERT: D 503 ASP cc_start: 0.8093 (m-30) cc_final: 0.7804 (m-30) REVERT: D 504 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: D 520 PHE cc_start: 0.8936 (t80) cc_final: 0.8495 (t80) REVERT: D 541 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7727 (mm) REVERT: D 553 SER cc_start: 0.9610 (m) cc_final: 0.9283 (p) REVERT: D 609 ASP cc_start: 0.8004 (m-30) cc_final: 0.7651 (t0) REVERT: D 631 LEU cc_start: 0.9204 (mp) cc_final: 0.8841 (mp) REVERT: D 694 LEU cc_start: 0.9415 (mm) cc_final: 0.9188 (mm) REVERT: D 700 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8718 (tt) REVERT: D 703 PHE cc_start: 0.8964 (t80) cc_final: 0.8643 (t80) REVERT: D 726 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7511 (mmmm) outliers start: 85 outliers final: 69 residues processed: 519 average time/residue: 0.2557 time to fit residues: 215.4519 Evaluate side-chains 528 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 448 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 670 PHE Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 190 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 298 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076240 restraints weight = 51539.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078620 restraints weight = 25835.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080172 restraints weight = 15766.813| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19924 Z= 0.165 Angle : 0.642 12.950 26964 Z= 0.306 Chirality : 0.041 0.316 3108 Planarity : 0.003 0.026 3324 Dihedral : 3.859 19.065 2656 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.18 % Allowed : 25.33 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.33 (0.17), residues: 2400 helix: 1.08 (0.14), residues: 1400 sheet: -1.07 (0.47), residues: 76 loop : -0.96 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 459 HIS 0.004 0.001 HIS A 443 PHE 0.025 0.001 PHE B 165 TYR 0.021 0.001 TYR D 563 ARG 0.004 0.000 ARG B 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.27 seconds wall clock time: 85 minutes 54.37 seconds (5154.37 seconds total)