Starting phenix.real_space_refine on Thu Feb 22 15:59:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m04_30029/02_2024/6m04_30029.pdb" } resolution = 4.36 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= 0.001 sd= 0.006 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 210 5.16 5 C 22556 2.51 5 N 5746 2.21 5 O 6154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 433": "NH1" <-> "NH2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 433": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Residue "E ARG 671": "NH1" <-> "NH2" Residue "E PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 137": "NH1" <-> "NH2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 433": "NH1" <-> "NH2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34666 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5773 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5773 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 17.49, per 1000 atoms: 0.50 Number of scatterers: 34666 At special positions: 0 Unit cell: (138.57, 171.35, 184.76, 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 210 16.00 O 6154 8.00 N 5746 7.00 C 22556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 354 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 354 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 354 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 354 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 354 " distance=2.02 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: 13.30 Conformation dependent library (CDL) restraints added in 5.9 seconds 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8348 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 45.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.184A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.527A pdb=" N LYS A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.543A pdb=" N TYR A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.559A pdb=" N LYS A 163 " --> pdb=" O TRP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 182 removed outlier: 3.525A pdb=" N LEU A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.936A pdb=" N SER A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.226A pdb=" N THR A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.707A pdb=" N LYS A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 390 Processing helix chain 'A' and resid 395 through 408 removed outlier: 4.156A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 4.066A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 removed outlier: 3.900A pdb=" N PHE A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 removed outlier: 4.057A pdb=" N LEU A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.590A pdb=" N LEU A 460 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.070A pdb=" N GLN A 511 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 removed outlier: 4.039A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.509A pdb=" N MET A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.824A pdb=" N ALA A 610 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 4.196A pdb=" N LYS A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.605A pdb=" N ILE A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 655 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 656 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 657 " --> pdb=" O ILE A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 657' Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.531A pdb=" N PHE A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 removed outlier: 3.942A pdb=" N ILE A 702 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.574A pdb=" N ILE A 748 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 749 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 removed outlier: 3.868A pdb=" N GLY A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 removed outlier: 3.534A pdb=" N CYS A 820 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.728A pdb=" N ALA B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.707A pdb=" N VAL B 26 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 Processing helix chain 'B' and resid 164 through 183 removed outlier: 3.518A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.974A pdb=" N VAL B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 4.038A pdb=" N THR B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 303 through 330 removed outlier: 4.322A pdb=" N ASN B 328 " --> pdb=" O CYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 390 removed outlier: 3.539A pdb=" N ILE B 390 " --> pdb=" O TRP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.708A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.573A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 removed outlier: 3.641A pdb=" N LEU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.754A pdb=" N LEU B 489 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.025A pdb=" N ILE B 509 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 511 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.900A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 576 through 580 removed outlier: 3.591A pdb=" N ILE B 579 " --> pdb=" O ASN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.728A pdb=" N ASP B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 609 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.619A pdb=" N LYS B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 633 " --> pdb=" O ASN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 682 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.717A pdb=" N ILE B 702 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 removed outlier: 4.296A pdb=" N PHE B 726 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 removed outlier: 4.381A pdb=" N LEU B 771 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 797 removed outlier: 3.592A pdb=" N VAL B 794 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 850 Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.633A pdb=" N VAL C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 157 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.871A pdb=" N LYS C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 182 removed outlier: 3.909A pdb=" N LEU C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.689A pdb=" N VAL C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.734A pdb=" N THR C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 296 removed outlier: 4.013A pdb=" N ALA C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 328 removed outlier: 3.935A pdb=" N LYS C 318 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 390 removed outlier: 3.891A pdb=" N ILE C 390 " --> pdb=" O TRP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 406 removed outlier: 3.746A pdb=" N GLU C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.872A pdb=" N MET C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 426 " --> pdb=" O MET C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 433 through 439 removed outlier: 3.780A pdb=" N PHE C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.363A pdb=" N LEU C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.839A pdb=" N GLN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 removed outlier: 4.310A pdb=" N LEU C 489 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.887A pdb=" N ILE C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 511 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 Processing helix chain 'C' and resid 576 through 581 removed outlier: 3.825A pdb=" N GLY C 580 " --> pdb=" O ASN C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 610 removed outlier: 4.367A pdb=" N VAL C 609 " --> pdb=" O ILE C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 4.008A pdb=" N ILE C 654 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 655 " --> pdb=" O HIS C 652 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 656 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 657 " --> pdb=" O ILE C 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 651 through 657' Processing helix chain 'C' and resid 677 through 682 Processing helix chain 'C' and resid 769 through 774 removed outlier: 3.551A pdb=" N CYS C 774 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.812A pdb=" N THR C 837 " --> pdb=" O HIS C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 849 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.527A pdb=" N LYS D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 removed outlier: 3.543A pdb=" N TYR D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.560A pdb=" N LYS D 163 " --> pdb=" O TRP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 182 removed outlier: 3.525A pdb=" N LEU D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.935A pdb=" N SER D 191 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.224A pdb=" N THR D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 302 through 332 removed outlier: 3.714A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE D 329 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 390 Processing helix chain 'D' and resid 395 through 408 removed outlier: 4.153A pdb=" N ASP D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 4.067A pdb=" N VAL D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 438 removed outlier: 3.900A pdb=" N PHE D 434 " --> pdb=" O TYR D 430 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 455 removed outlier: 4.062A pdb=" N LEU D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.589A pdb=" N LEU D 460 " --> pdb=" O PHE D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 512 removed outlier: 4.070A pdb=" N GLN D 511 " --> pdb=" O LYS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 537 removed outlier: 4.040A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.509A pdb=" N MET D 578 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 610 removed outlier: 3.825A pdb=" N ALA D 610 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 633 removed outlier: 4.196A pdb=" N LYS D 633 " --> pdb=" O ASN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 657 removed outlier: 3.605A pdb=" N ILE D 654 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 655 " --> pdb=" O HIS D 652 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER D 656 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 657 " --> pdb=" O ILE D 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 651 through 657' Processing helix chain 'D' and resid 675 through 682 removed outlier: 3.531A pdb=" N PHE D 679 " --> pdb=" O GLU D 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 681 " --> pdb=" O ILE D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.942A pdb=" N ILE D 702 " --> pdb=" O PRO D 699 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.575A pdb=" N ILE D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 749 " --> pdb=" O ILE D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 797 removed outlier: 3.870A pdb=" N GLY D 795 " --> pdb=" O PRO D 791 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 820 removed outlier: 3.533A pdb=" N CYS D 820 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 849 Processing helix chain 'E' and resid 4 through 11 removed outlier: 3.683A pdb=" N ALA E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.707A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 157 Processing helix chain 'E' and resid 164 through 183 removed outlier: 3.517A pdb=" N LEU E 168 " --> pdb=" O TYR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.975A pdb=" N VAL E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 214 removed outlier: 4.038A pdb=" N THR E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 298 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 303 through 330 removed outlier: 4.322A pdb=" N ASN E 328 " --> pdb=" O CYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 390 removed outlier: 3.539A pdb=" N ILE E 390 " --> pdb=" O TRP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 3.717A pdb=" N PHE E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 Processing helix chain 'E' and resid 428 through 435 removed outlier: 3.573A pdb=" N GLY E 435 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 454 removed outlier: 3.641A pdb=" N LEU E 446 " --> pdb=" O SER E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 484 through 489 removed outlier: 3.754A pdb=" N LEU E 489 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 removed outlier: 4.025A pdb=" N ILE E 509 " --> pdb=" O PRO E 506 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 511 " --> pdb=" O LYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 538 removed outlier: 3.900A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 558 Processing helix chain 'E' and resid 576 through 580 removed outlier: 3.591A pdb=" N ILE E 579 " --> pdb=" O ASN E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 605 through 610 removed outlier: 3.728A pdb=" N ASP E 608 " --> pdb=" O ASN E 605 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL E 609 " --> pdb=" O ILE E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 634 removed outlier: 4.619A pdb=" N LYS E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 633 " --> pdb=" O ASN E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 682 Processing helix chain 'E' and resid 699 through 704 removed outlier: 3.717A pdb=" N ILE E 702 " --> pdb=" O PRO E 699 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 703 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 728 removed outlier: 4.298A pdb=" N PHE E 726 " --> pdb=" O VAL E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 773 removed outlier: 4.381A pdb=" N LEU E 771 " --> pdb=" O PRO E 768 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 772 " --> pdb=" O LYS E 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 797 removed outlier: 3.592A pdb=" N VAL E 794 " --> pdb=" O PRO E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 850 Processing helix chain 'F' and resid 4 through 12 removed outlier: 3.563A pdb=" N ALA F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.635A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 157 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.872A pdb=" N LYS F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 182 removed outlier: 3.910A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.689A pdb=" N VAL F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 removed outlier: 3.734A pdb=" N THR F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 296 removed outlier: 4.014A pdb=" N ALA F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 328 removed outlier: 3.936A pdb=" N LYS F 318 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 390 removed outlier: 3.892A pdb=" N ILE F 390 " --> pdb=" O TRP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 406 removed outlier: 3.746A pdb=" N GLU F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 427 removed outlier: 3.872A pdb=" N MET F 422 " --> pdb=" O PHE F 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 426 " --> pdb=" O MET F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 439 removed outlier: 3.780A pdb=" N PHE F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 445 through 455 removed outlier: 4.364A pdb=" N LEU F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 464 removed outlier: 3.839A pdb=" N GLN F 462 " --> pdb=" O GLU F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 removed outlier: 4.310A pdb=" N LEU F 489 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.887A pdb=" N ILE F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN F 511 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 558 Processing helix chain 'F' and resid 576 through 581 removed outlier: 3.822A pdb=" N GLY F 580 " --> pdb=" O ASN F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 610 removed outlier: 4.367A pdb=" N VAL F 609 " --> pdb=" O ILE F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 657 removed outlier: 4.009A pdb=" N ILE F 654 " --> pdb=" O PRO F 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 655 " --> pdb=" O HIS F 652 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER F 656 " --> pdb=" O ALA F 653 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 657 " --> pdb=" O ILE F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 657' Processing helix chain 'F' and resid 677 through 682 Processing helix chain 'F' and resid 769 through 774 removed outlier: 3.551A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 792 through 797 Processing helix chain 'F' and resid 814 through 819 Processing helix chain 'F' and resid 831 through 837 removed outlier: 3.813A pdb=" N THR F 837 " --> pdb=" O HIS F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 849 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.823A pdb=" N LEU A 542 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 565 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 593 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 616 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 662 through 664 removed outlier: 5.632A pdb=" N LEU A 663 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 688 " --> pdb=" O TYR A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 757 removed outlier: 6.695A pdb=" N LEU A 757 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 803 " --> pdb=" O LYS A 825 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.735A pdb=" N GLN B 472 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU B 498 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 495 " --> pdb=" O HIS B 519 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N CYS B 521 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 497 " --> pdb=" O CYS B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 592 through 595 removed outlier: 6.113A pdb=" N LEU B 593 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 616 " --> pdb=" O GLU B 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 687 through 688 removed outlier: 3.524A pdb=" N LEU B 688 " --> pdb=" O SER B 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 removed outlier: 7.594A pdb=" N VAL B 736 " --> pdb=" O THR B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 779 through 781 removed outlier: 5.979A pdb=" N LEU B 780 " --> pdb=" O GLU B 804 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 803 " --> pdb=" O LYS B 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 56 removed outlier: 3.744A pdb=" N GLU C 353 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 471 through 473 removed outlier: 6.621A pdb=" N GLN C 472 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU C 498 " --> pdb=" O GLN C 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 541 through 543 removed outlier: 6.510A pdb=" N LEU C 542 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 565 " --> pdb=" O HIS C 594 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 593 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 616 " --> pdb=" O GLU C 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 759 through 760 removed outlier: 6.763A pdb=" N ILE C 759 " --> pdb=" O GLY C 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB8, first strand: chain 'D' and resid 471 through 472 Processing sheet with id=AB9, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.823A pdb=" N LEU D 542 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU D 565 " --> pdb=" O HIS D 594 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU D 593 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 616 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 662 through 664 removed outlier: 5.632A pdb=" N LEU D 663 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU D 688 " --> pdb=" O TYR D 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 756 through 757 removed outlier: 6.695A pdb=" N LEU D 757 " --> pdb=" O ASN D 781 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 803 " --> pdb=" O LYS D 825 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'E' and resid 471 through 472 removed outlier: 6.735A pdb=" N GLN E 472 " --> pdb=" O LYS E 496 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU E 498 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU E 495 " --> pdb=" O HIS E 519 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N CYS E 521 " --> pdb=" O LEU E 495 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 497 " --> pdb=" O CYS E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 592 through 595 removed outlier: 6.113A pdb=" N LEU E 593 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU E 616 " --> pdb=" O GLU E 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 687 through 688 removed outlier: 3.525A pdb=" N LEU E 688 " --> pdb=" O SER E 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 736 through 737 removed outlier: 7.594A pdb=" N VAL E 736 " --> pdb=" O THR E 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 779 through 781 removed outlier: 5.979A pdb=" N LEU E 780 " --> pdb=" O GLU E 804 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU E 803 " --> pdb=" O LYS E 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 52 through 56 removed outlier: 3.744A pdb=" N GLU F 353 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 471 through 473 removed outlier: 6.622A pdb=" N GLN F 472 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU F 498 " --> pdb=" O GLN F 472 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 541 through 543 removed outlier: 6.509A pdb=" N LEU F 542 " --> pdb=" O TYR F 566 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU F 565 " --> pdb=" O HIS F 594 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 593 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU F 616 " --> pdb=" O GLU F 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 759 through 760 removed outlier: 6.763A pdb=" N ILE F 759 " --> pdb=" O GLY F 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 1182 hydrogen bonds defined for protein. 3330 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: 10.99 Time building geometry restraints manager: 14.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9364 1.33 - 1.45: 5915 1.45 - 1.57: 19845 1.57 - 1.69: 2 1.69 - 1.81: 306 Bond restraints: 35432 Sorted by residual: bond pdb=" CA LEU D 782 " pdb=" CB LEU D 782 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.53e-02 4.27e+03 5.81e+00 bond pdb=" CA LEU A 782 " pdb=" CB LEU A 782 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.53e-02 4.27e+03 5.81e+00 bond pdb=" C LYS A 185 " pdb=" N TYR A 186 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.93e+00 bond pdb=" C LYS D 185 " pdb=" N TYR D 186 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.93e+00 bond pdb=" CB PHE E 294 " pdb=" CG PHE E 294 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.71e+00 ... (remaining 35427 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.41: 512 104.41 - 111.88: 15736 111.88 - 119.35: 14148 119.35 - 126.82: 17112 126.82 - 134.29: 510 Bond angle restraints: 48018 Sorted by residual: angle pdb=" N THR F 686 " pdb=" CA THR F 686 " pdb=" C THR F 686 " ideal model delta sigma weight residual 114.56 108.46 6.10 1.27e+00 6.20e-01 2.31e+01 angle pdb=" N THR C 686 " pdb=" CA THR C 686 " pdb=" C THR C 686 " ideal model delta sigma weight residual 114.56 108.52 6.04 1.27e+00 6.20e-01 2.26e+01 angle pdb=" C PHE E 352 " pdb=" N GLU E 353 " pdb=" CA GLU E 353 " ideal model delta sigma weight residual 121.85 113.59 8.26 1.77e+00 3.19e-01 2.18e+01 angle pdb=" C PHE B 352 " pdb=" N GLU B 353 " pdb=" CA GLU B 353 " ideal model delta sigma weight residual 121.85 113.59 8.26 1.77e+00 3.19e-01 2.18e+01 angle pdb=" CA TYR F 30 " pdb=" CB TYR F 30 " pdb=" CG TYR F 30 " ideal model delta sigma weight residual 113.90 122.05 -8.15 1.80e+00 3.09e-01 2.05e+01 ... (remaining 48013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 19005 15.78 - 31.56: 1914 31.56 - 47.34: 473 47.34 - 63.13: 36 63.13 - 78.91: 28 Dihedral angle restraints: 21456 sinusoidal: 8712 harmonic: 12744 Sorted by residual: dihedral pdb=" CA PHE B 182 " pdb=" C PHE B 182 " pdb=" N TRP B 183 " pdb=" CA TRP B 183 " ideal model delta harmonic sigma weight residual 180.00 143.88 36.12 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA PHE E 182 " pdb=" C PHE E 182 " pdb=" N TRP E 183 " pdb=" CA TRP E 183 " ideal model delta harmonic sigma weight residual 180.00 143.90 36.10 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA LYS F 504 " pdb=" C LYS F 504 " pdb=" N ILE F 505 " pdb=" CA ILE F 505 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.50e+01 ... (remaining 21453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4800 0.088 - 0.177: 736 0.177 - 0.265: 70 0.265 - 0.353: 6 0.353 - 0.441: 8 Chirality restraints: 5620 Sorted by residual: chirality pdb=" CB ILE D 759 " pdb=" CA ILE D 759 " pdb=" CG1 ILE D 759 " pdb=" CG2 ILE D 759 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE E 746 " pdb=" CA ILE E 746 " pdb=" CG1 ILE E 746 " pdb=" CG2 ILE E 746 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.31e+00 ... (remaining 5617 not shown) Planarity restraints: 5960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 500 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO F 501 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO F 501 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 501 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 500 " 0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO C 501 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 501 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 501 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 505 " 0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO C 506 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 506 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 506 " 0.048 5.00e-02 4.00e+02 ... (remaining 5957 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6737 2.78 - 3.31: 34116 3.31 - 3.84: 59340 3.84 - 4.37: 66372 4.37 - 4.90: 108567 Nonbonded interactions: 275132 Sorted by model distance: nonbonded pdb=" O LEU C 803 " pdb=" OG SER C 826 " model vdw 2.245 2.440 nonbonded pdb=" O LEU F 803 " pdb=" OG SER F 826 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR D 17 " pdb=" OE1 GLU D 194 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR A 17 " pdb=" OE1 GLU A 194 " model vdw 2.281 2.440 nonbonded pdb=" O MET A 177 " pdb=" OG SER A 180 " model vdw 2.288 2.440 ... (remaining 275127 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' and (resid 2 through 58 or resid 135 through 850)) selection = (chain 'B' and (resid 2 through 58 or resid 135 through 850)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 58 or resid 135 through 850)) selection = (chain 'E' and (resid 2 through 58 or resid 135 through 850)) selection = chain 'F' } 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: 0.730 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: 4.810 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 83.810 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.006 0.078 35432 Z= 0.376 Angle : 1.279 15.669 48018 Z= 0.639 Chirality : 0.065 0.441 5620 Planarity : 0.008 0.090 5960 Dihedral : 13.634 78.907 13090 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.51 % Favored : 87.49 % Rotamer: Outliers : 1.93 % Allowed : 9.50 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -5.02 (0.10), residues: 4246 helix: -2.94 (0.09), residues: 1768 sheet: -3.15 (0.27), residues: 262 loop : -3.79 (0.10), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 208 HIS 0.019 0.003 HIS E 543 PHE 0.048 0.003 PHE B 182 TYR 0.031 0.004 TYR C 146 ARG 0.016 0.001 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 815 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8782 (t) cc_final: 0.8361 (p) REVERT: A 28 MET cc_start: 0.8564 (mtt) cc_final: 0.8289 (mtt) REVERT: A 329 PHE cc_start: 0.8290 (p90) cc_final: 0.8014 (p90) REVERT: A 358 MET cc_start: 0.8090 (mmt) cc_final: 0.7865 (mmm) REVERT: A 420 LEU cc_start: 0.8741 (tp) cc_final: 0.8527 (tp) REVERT: A 478 MET cc_start: 0.6139 (tpt) cc_final: 0.5527 (tpp) REVERT: A 480 SER cc_start: 0.8200 (p) cc_final: 0.7940 (t) REVERT: A 628 LEU cc_start: 0.7572 (mm) cc_final: 0.6957 (pp) REVERT: A 632 LYS cc_start: 0.7934 (pttp) cc_final: 0.7622 (mmtt) REVERT: A 743 MET cc_start: 0.5606 (tpt) cc_final: 0.5312 (mtp) REVERT: B 152 MET cc_start: 0.8203 (tpp) cc_final: 0.7931 (tpp) REVERT: B 171 ILE cc_start: 0.9088 (mm) cc_final: 0.8810 (mm) REVERT: B 184 PHE cc_start: 0.7718 (t80) cc_final: 0.7468 (t80) REVERT: B 351 VAL cc_start: 0.8425 (t) cc_final: 0.7971 (p) REVERT: B 367 ILE cc_start: 0.9204 (pt) cc_final: 0.8980 (tt) REVERT: B 542 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6798 (pt) REVERT: B 558 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7692 (pt) REVERT: B 568 ILE cc_start: 0.8514 (pp) cc_final: 0.7776 (pt) REVERT: B 617 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 152 MET cc_start: 0.8584 (tpp) cc_final: 0.8264 (tpp) REVERT: C 453 HIS cc_start: 0.8426 (t70) cc_final: 0.8061 (m170) REVERT: C 458 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8204 (tm-30) REVERT: C 462 GLN cc_start: 0.8745 (mp10) cc_final: 0.8379 (mp10) REVERT: C 464 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6786 (mp) REVERT: C 511 GLN cc_start: 0.8380 (pt0) cc_final: 0.7820 (tm-30) REVERT: C 567 LEU cc_start: 0.9342 (tm) cc_final: 0.9097 (tt) REVERT: C 665 LEU cc_start: 0.2226 (OUTLIER) cc_final: 0.1997 (pt) REVERT: C 782 LEU cc_start: 0.7516 (pp) cc_final: 0.7239 (mp) REVERT: D 26 VAL cc_start: 0.8784 (t) cc_final: 0.8372 (p) REVERT: D 28 MET cc_start: 0.8572 (mtt) cc_final: 0.8282 (mtt) REVERT: D 329 PHE cc_start: 0.8290 (p90) cc_final: 0.8016 (p90) REVERT: D 358 MET cc_start: 0.8103 (mmt) cc_final: 0.7878 (mmm) REVERT: D 420 LEU cc_start: 0.8740 (tp) cc_final: 0.8516 (tp) REVERT: D 478 MET cc_start: 0.6152 (tpt) cc_final: 0.5535 (tpp) REVERT: D 480 SER cc_start: 0.8186 (p) cc_final: 0.7946 (t) REVERT: D 628 LEU cc_start: 0.7563 (mm) cc_final: 0.6957 (pp) REVERT: D 632 LYS cc_start: 0.7884 (pttp) cc_final: 0.7553 (mmtt) REVERT: D 743 MET cc_start: 0.5603 (tpt) cc_final: 0.5304 (mtp) REVERT: E 152 MET cc_start: 0.8209 (tpp) cc_final: 0.7937 (tpp) REVERT: E 171 ILE cc_start: 0.9088 (mm) cc_final: 0.8812 (mm) REVERT: E 184 PHE cc_start: 0.7719 (t80) cc_final: 0.7475 (t80) REVERT: E 351 VAL cc_start: 0.8429 (t) cc_final: 0.7981 (p) REVERT: E 367 ILE cc_start: 0.9201 (pt) cc_final: 0.8975 (tt) REVERT: E 542 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6789 (pt) REVERT: E 558 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7690 (pt) REVERT: E 568 ILE cc_start: 0.8512 (pp) cc_final: 0.7778 (pt) REVERT: E 617 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.7752 (p) REVERT: F 152 MET cc_start: 0.8591 (tpp) cc_final: 0.8255 (tpp) REVERT: F 453 HIS cc_start: 0.8424 (t70) cc_final: 0.8056 (m170) REVERT: F 464 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6392 (mp) REVERT: F 491 ASP cc_start: 0.7815 (p0) cc_final: 0.7276 (p0) REVERT: F 511 GLN cc_start: 0.8380 (pt0) cc_final: 0.7815 (tm-30) REVERT: F 567 LEU cc_start: 0.9343 (tm) cc_final: 0.9097 (tt) REVERT: F 665 LEU cc_start: 0.2154 (OUTLIER) cc_final: 0.1946 (pt) REVERT: F 782 LEU cc_start: 0.7518 (pp) cc_final: 0.7240 (mp) outliers start: 76 outliers final: 12 residues processed: 883 average time/residue: 0.4473 time to fit residues: 637.7940 Evaluate side-chains 478 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 456 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 333 optimal weight: 0.2980 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 386 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 444 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 692 HIS A 755 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN B 605 ASN B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 576 ASN ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 444 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 755 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN E 605 ASN E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN F 784 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35432 Z= 0.222 Angle : 0.789 11.430 48018 Z= 0.397 Chirality : 0.047 0.201 5620 Planarity : 0.006 0.063 5960 Dihedral : 7.241 31.156 4522 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.91 (0.11), residues: 4246 helix: -1.77 (0.11), residues: 1774 sheet: -2.65 (0.28), residues: 270 loop : -3.41 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 208 HIS 0.010 0.001 HIS D 543 PHE 0.034 0.002 PHE E 321 TYR 0.029 0.002 TYR F 30 ARG 0.008 0.001 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 608 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6862 (pp30) cc_final: 0.6383 (pp30) REVERT: A 37 MET cc_start: 0.8163 (tmm) cc_final: 0.7885 (tmm) REVERT: A 185 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8484 (pttp) REVERT: A 329 PHE cc_start: 0.8219 (p90) cc_final: 0.7989 (p90) REVERT: A 353 GLU cc_start: 0.8183 (pp20) cc_final: 0.7954 (pp20) REVERT: A 420 LEU cc_start: 0.8804 (tp) cc_final: 0.8497 (tp) REVERT: A 478 MET cc_start: 0.5844 (tpt) cc_final: 0.4749 (ttt) REVERT: A 529 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6386 (pm20) REVERT: A 575 ASN cc_start: 0.8284 (m-40) cc_final: 0.7982 (p0) REVERT: A 576 ASN cc_start: 0.5732 (m110) cc_final: 0.4800 (m-40) REVERT: A 628 LEU cc_start: 0.7309 (mm) cc_final: 0.6602 (pp) REVERT: A 635 MET cc_start: 0.7794 (mtp) cc_final: 0.7475 (mmm) REVERT: A 743 MET cc_start: 0.4169 (tpt) cc_final: 0.3860 (mtp) REVERT: B 20 LEU cc_start: 0.8760 (tt) cc_final: 0.8551 (tp) REVERT: B 171 ILE cc_start: 0.9331 (mm) cc_final: 0.9099 (mm) REVERT: B 185 LYS cc_start: 0.8708 (mmmt) cc_final: 0.7217 (tmtt) REVERT: B 195 HIS cc_start: 0.8311 (t-90) cc_final: 0.7983 (t-170) REVERT: B 204 PHE cc_start: 0.8111 (t80) cc_final: 0.7770 (t80) REVERT: B 289 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8035 (mm-30) REVERT: B 294 PHE cc_start: 0.7903 (m-80) cc_final: 0.7573 (m-80) REVERT: B 358 MET cc_start: 0.7241 (mmp) cc_final: 0.6898 (mmp) REVERT: B 373 ILE cc_start: 0.9428 (mm) cc_final: 0.8867 (tp) REVERT: B 657 LEU cc_start: 0.3626 (OUTLIER) cc_final: 0.3348 (pp) REVERT: B 832 ASP cc_start: 0.8318 (p0) cc_final: 0.7797 (p0) REVERT: C 422 MET cc_start: 0.8886 (tmm) cc_final: 0.8578 (tmm) REVERT: C 462 GLN cc_start: 0.8795 (mp10) cc_final: 0.7856 (pp30) REVERT: C 478 MET cc_start: 0.8198 (tmm) cc_final: 0.7902 (tmm) REVERT: C 484 ASP cc_start: 0.8252 (m-30) cc_final: 0.7494 (m-30) REVERT: C 511 GLN cc_start: 0.8693 (pt0) cc_final: 0.8209 (pp30) REVERT: C 782 LEU cc_start: 0.7695 (pp) cc_final: 0.7493 (mp) REVERT: D 37 MET cc_start: 0.8160 (tmm) cc_final: 0.7892 (tmm) REVERT: D 185 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8457 (pttp) REVERT: D 329 PHE cc_start: 0.8250 (p90) cc_final: 0.7986 (p90) REVERT: D 353 GLU cc_start: 0.8181 (pp20) cc_final: 0.7954 (pp20) REVERT: D 420 LEU cc_start: 0.8805 (tp) cc_final: 0.8520 (tp) REVERT: D 478 MET cc_start: 0.5846 (tpt) cc_final: 0.4778 (ttt) REVERT: D 628 LEU cc_start: 0.7307 (mm) cc_final: 0.6741 (pp) REVERT: D 635 MET cc_start: 0.7778 (mtp) cc_final: 0.7339 (mmm) REVERT: D 743 MET cc_start: 0.4149 (tpt) cc_final: 0.3875 (mtp) REVERT: E 20 LEU cc_start: 0.8754 (tt) cc_final: 0.8552 (tp) REVERT: E 171 ILE cc_start: 0.9326 (mm) cc_final: 0.9099 (mm) REVERT: E 185 LYS cc_start: 0.8704 (mmmt) cc_final: 0.7219 (tmtt) REVERT: E 195 HIS cc_start: 0.8312 (t-90) cc_final: 0.7990 (t-170) REVERT: E 204 PHE cc_start: 0.8171 (t80) cc_final: 0.7822 (t80) REVERT: E 289 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8036 (mm-30) REVERT: E 294 PHE cc_start: 0.7901 (m-80) cc_final: 0.7572 (m-80) REVERT: E 358 MET cc_start: 0.7238 (mmp) cc_final: 0.6864 (mmp) REVERT: E 373 ILE cc_start: 0.9430 (mm) cc_final: 0.8855 (tp) REVERT: E 489 LEU cc_start: 0.6296 (mp) cc_final: 0.6022 (mp) REVERT: E 578 MET cc_start: 0.4547 (mmt) cc_final: 0.4254 (mpp) REVERT: E 657 LEU cc_start: 0.3613 (OUTLIER) cc_final: 0.3338 (pp) REVERT: E 832 ASP cc_start: 0.7890 (p0) cc_final: 0.7428 (p0) REVERT: F 177 MET cc_start: 0.6530 (ttt) cc_final: 0.6279 (ttt) REVERT: F 422 MET cc_start: 0.8880 (tmm) cc_final: 0.8590 (tmm) REVERT: F 478 MET cc_start: 0.8181 (tmm) cc_final: 0.7889 (tmm) REVERT: F 484 ASP cc_start: 0.8261 (m-30) cc_final: 0.7524 (m-30) REVERT: F 491 ASP cc_start: 0.7870 (p0) cc_final: 0.7626 (p0) REVERT: F 511 GLN cc_start: 0.8689 (pt0) cc_final: 0.8125 (pp30) outliers start: 9 outliers final: 2 residues processed: 617 average time/residue: 0.4599 time to fit residues: 468.3056 Evaluate side-chains 415 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 411 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 263 optimal weight: 0.0010 chunk 106 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 chunk 418 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 384 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 310 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 283 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS C 421 HIS C 453 HIS ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 195 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 598 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS E 283 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS F 421 HIS F 453 HIS F 463 HIS ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35432 Z= 0.224 Angle : 0.763 12.090 48018 Z= 0.379 Chirality : 0.046 0.185 5620 Planarity : 0.005 0.057 5960 Dihedral : 6.744 29.673 4522 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.18 % Allowed : 7.54 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.12), residues: 4246 helix: -1.29 (0.11), residues: 1818 sheet: -2.06 (0.34), residues: 226 loop : -3.35 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 208 HIS 0.010 0.001 HIS F 172 PHE 0.025 0.002 PHE D 546 TYR 0.029 0.002 TYR F 30 ARG 0.005 0.001 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 539 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6895 (pp30) cc_final: 0.6517 (pp30) REVERT: A 19 ILE cc_start: 0.8391 (tp) cc_final: 0.7998 (mm) REVERT: A 185 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8552 (pttp) REVERT: A 420 LEU cc_start: 0.8855 (tp) cc_final: 0.8488 (tp) REVERT: A 529 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6546 (pm20) REVERT: A 575 ASN cc_start: 0.8236 (m-40) cc_final: 0.7751 (p0) REVERT: A 576 ASN cc_start: 0.5684 (m110) cc_final: 0.5051 (m110) REVERT: A 628 LEU cc_start: 0.7315 (mm) cc_final: 0.6621 (pp) REVERT: A 635 MET cc_start: 0.7748 (mtp) cc_final: 0.6965 (tpp) REVERT: A 743 MET cc_start: 0.4175 (tpt) cc_final: 0.3897 (ttp) REVERT: B 55 LEU cc_start: 0.8841 (pt) cc_final: 0.8599 (pt) REVERT: B 204 PHE cc_start: 0.8022 (t80) cc_final: 0.7683 (t80) REVERT: B 289 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7904 (mm-30) REVERT: B 358 MET cc_start: 0.7170 (mmp) cc_final: 0.6924 (mmp) REVERT: B 373 ILE cc_start: 0.9470 (mm) cc_final: 0.8907 (tp) REVERT: B 471 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7816 (ptmt) REVERT: B 492 LEU cc_start: 0.7937 (mm) cc_final: 0.7390 (mt) REVERT: B 545 LYS cc_start: 0.8305 (ptmm) cc_final: 0.7913 (ptmm) REVERT: B 568 ILE cc_start: 0.8114 (pt) cc_final: 0.7880 (pt) REVERT: B 593 LEU cc_start: 0.9025 (pp) cc_final: 0.8688 (pp) REVERT: B 832 ASP cc_start: 0.8206 (p0) cc_final: 0.8004 (p0) REVERT: C 458 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 462 GLN cc_start: 0.8820 (mp10) cc_final: 0.8470 (mp10) REVERT: C 476 LEU cc_start: 0.3790 (OUTLIER) cc_final: 0.3583 (tt) REVERT: C 478 MET cc_start: 0.8307 (tmm) cc_final: 0.7929 (tmm) REVERT: C 484 ASP cc_start: 0.8045 (m-30) cc_final: 0.7355 (m-30) REVERT: C 511 GLN cc_start: 0.8661 (pt0) cc_final: 0.7979 (pp30) REVERT: C 567 LEU cc_start: 0.9288 (tt) cc_final: 0.9014 (tt) REVERT: D 19 ILE cc_start: 0.8485 (tp) cc_final: 0.8050 (mm) REVERT: D 185 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8511 (pttp) REVERT: D 358 MET cc_start: 0.7949 (mmm) cc_final: 0.7730 (mmp) REVERT: D 420 LEU cc_start: 0.8849 (tp) cc_final: 0.8447 (tp) REVERT: D 628 LEU cc_start: 0.7390 (mm) cc_final: 0.6582 (pp) REVERT: D 632 LYS cc_start: 0.7745 (pttp) cc_final: 0.7291 (mmtt) REVERT: D 635 MET cc_start: 0.7747 (mtp) cc_final: 0.6953 (tpp) REVERT: D 743 MET cc_start: 0.4191 (tpt) cc_final: 0.3914 (ttp) REVERT: E 55 LEU cc_start: 0.8839 (pt) cc_final: 0.8585 (pt) REVERT: E 204 PHE cc_start: 0.8107 (t80) cc_final: 0.7768 (t80) REVERT: E 289 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7893 (mm-30) REVERT: E 340 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7153 (mmmm) REVERT: E 358 MET cc_start: 0.7149 (mmp) cc_final: 0.6945 (mmp) REVERT: E 373 ILE cc_start: 0.9456 (mm) cc_final: 0.8892 (tp) REVERT: E 471 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7819 (ptmt) REVERT: E 512 MET cc_start: 0.7211 (tpp) cc_final: 0.6805 (tpp) REVERT: E 545 LYS cc_start: 0.8313 (ptmm) cc_final: 0.7932 (ptmm) REVERT: E 568 ILE cc_start: 0.8137 (pt) cc_final: 0.7879 (pt) REVERT: E 593 LEU cc_start: 0.9019 (pp) cc_final: 0.8686 (pp) REVERT: E 773 LYS cc_start: 0.7536 (tmtt) cc_final: 0.7252 (ptmm) REVERT: E 832 ASP cc_start: 0.8020 (p0) cc_final: 0.7778 (p0) REVERT: F 177 MET cc_start: 0.6696 (ttt) cc_final: 0.6449 (ttt) REVERT: F 466 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7724 (mmt180) REVERT: F 478 MET cc_start: 0.8276 (tmm) cc_final: 0.7895 (tmm) REVERT: F 484 ASP cc_start: 0.8074 (m-30) cc_final: 0.7702 (m-30) REVERT: F 491 ASP cc_start: 0.8082 (p0) cc_final: 0.7795 (p0) REVERT: F 511 GLN cc_start: 0.8639 (pt0) cc_final: 0.8005 (pp30) REVERT: F 548 ASP cc_start: 0.8564 (p0) cc_final: 0.7979 (p0) REVERT: F 567 LEU cc_start: 0.9303 (tt) cc_final: 0.9041 (tt) REVERT: F 648 GLU cc_start: 0.7408 (pm20) cc_final: 0.7108 (pm20) REVERT: F 757 LEU cc_start: 0.6705 (mm) cc_final: 0.6494 (mm) REVERT: F 782 LEU cc_start: 0.7782 (mp) cc_final: 0.7199 (pp) outliers start: 7 outliers final: 0 residues processed: 546 average time/residue: 0.4276 time to fit residues: 387.3332 Evaluate side-chains 407 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.0570 chunk 291 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 388 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 368 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS B 692 HIS ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 HIS ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 HIS ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 681 HIS E 692 HIS ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 612 HIS ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35432 Z= 0.273 Angle : 0.790 14.534 48018 Z= 0.391 Chirality : 0.047 0.220 5620 Planarity : 0.005 0.055 5960 Dihedral : 6.639 31.661 4522 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.29 (0.12), residues: 4246 helix: -1.04 (0.12), residues: 1808 sheet: -1.99 (0.36), residues: 206 loop : -3.33 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 183 HIS 0.009 0.002 HIS C 172 PHE 0.037 0.002 PHE B 182 TYR 0.033 0.002 TYR C 30 ARG 0.007 0.001 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 511 time to evaluate : 4.064 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: A 14 GLN cc_start: 0.6905 (pp30) cc_final: 0.6607 (pp30) REVERT: A 185 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8619 (pttp) REVERT: A 420 LEU cc_start: 0.8786 (tp) cc_final: 0.8364 (tp) REVERT: A 512 MET cc_start: 0.7043 (mmt) cc_final: 0.6706 (mmt) REVERT: A 529 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6658 (pm20) REVERT: A 546 PHE cc_start: 0.8539 (m-10) cc_final: 0.8205 (m-80) REVERT: A 575 ASN cc_start: 0.8231 (m-40) cc_final: 0.7760 (p0) REVERT: A 576 ASN cc_start: 0.5673 (m110) cc_final: 0.5007 (m110) REVERT: A 628 LEU cc_start: 0.7370 (mm) cc_final: 0.6650 (pp) REVERT: A 743 MET cc_start: 0.4196 (tpt) cc_final: 0.3937 (ttp) REVERT: A 832 ASP cc_start: 0.8451 (m-30) cc_final: 0.8099 (t0) REVERT: B 24 TRP cc_start: 0.8750 (p90) cc_final: 0.8237 (p90) REVERT: B 35 MET cc_start: 0.8220 (tmm) cc_final: 0.7892 (tmm) REVERT: B 55 LEU cc_start: 0.9072 (pt) cc_final: 0.8668 (pp) REVERT: B 204 PHE cc_start: 0.7959 (t80) cc_final: 0.7659 (t80) REVERT: B 289 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7880 (mm-30) REVERT: B 471 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7877 (ptmt) REVERT: B 478 MET cc_start: 0.6780 (tpt) cc_final: 0.6542 (tpt) REVERT: B 492 LEU cc_start: 0.8038 (mm) cc_final: 0.7721 (mm) REVERT: B 512 MET cc_start: 0.7522 (tpp) cc_final: 0.6935 (tpp) REVERT: B 634 MET cc_start: 0.8797 (tmm) cc_final: 0.8348 (tmm) REVERT: C 152 MET cc_start: 0.8449 (tpp) cc_final: 0.8230 (tpp) REVERT: C 177 MET cc_start: 0.7337 (ttt) cc_final: 0.7037 (ttt) REVERT: C 478 MET cc_start: 0.8325 (tmm) cc_final: 0.7931 (tmm) REVERT: C 484 ASP cc_start: 0.7914 (m-30) cc_final: 0.7276 (m-30) REVERT: C 511 GLN cc_start: 0.8547 (pt0) cc_final: 0.7936 (tm-30) REVERT: C 567 LEU cc_start: 0.9268 (tt) cc_final: 0.8969 (tt) REVERT: D 185 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8514 (pttp) REVERT: D 420 LEU cc_start: 0.8787 (tp) cc_final: 0.8362 (tp) REVERT: D 512 MET cc_start: 0.6844 (mmt) cc_final: 0.6490 (mmt) REVERT: D 546 PHE cc_start: 0.8560 (m-10) cc_final: 0.8199 (m-80) REVERT: D 628 LEU cc_start: 0.7569 (mm) cc_final: 0.6821 (pp) REVERT: D 743 MET cc_start: 0.4179 (tpt) cc_final: 0.3911 (ttp) REVERT: D 832 ASP cc_start: 0.8454 (m-30) cc_final: 0.8088 (t0) REVERT: E 6 GLU cc_start: 0.8073 (tp30) cc_final: 0.7764 (tp30) REVERT: E 35 MET cc_start: 0.8247 (tmm) cc_final: 0.7927 (tmm) REVERT: E 55 LEU cc_start: 0.9080 (pt) cc_final: 0.8659 (pp) REVERT: E 164 TYR cc_start: 0.8493 (m-10) cc_final: 0.8292 (m-10) REVERT: E 204 PHE cc_start: 0.8056 (t80) cc_final: 0.7718 (t80) REVERT: E 289 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7870 (mm-30) REVERT: E 471 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7856 (pttm) REVERT: E 478 MET cc_start: 0.6770 (tpt) cc_final: 0.6526 (tpt) REVERT: E 512 MET cc_start: 0.7353 (tpp) cc_final: 0.6707 (tpp) REVERT: E 634 MET cc_start: 0.8806 (tmm) cc_final: 0.8354 (tmm) REVERT: E 773 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7371 (ptmm) REVERT: E 832 ASP cc_start: 0.8057 (p0) cc_final: 0.7738 (p0) REVERT: F 152 MET cc_start: 0.8481 (tpp) cc_final: 0.8223 (tpp) REVERT: F 177 MET cc_start: 0.6781 (ttt) cc_final: 0.6486 (ttt) REVERT: F 478 MET cc_start: 0.8288 (tmm) cc_final: 0.7946 (tmm) REVERT: F 484 ASP cc_start: 0.7922 (m-30) cc_final: 0.7272 (m-30) REVERT: F 511 GLN cc_start: 0.8546 (pt0) cc_final: 0.8012 (pp30) REVERT: F 548 ASP cc_start: 0.8609 (p0) cc_final: 0.7989 (p0) REVERT: F 567 LEU cc_start: 0.9308 (tt) cc_final: 0.8990 (tt) REVERT: F 782 LEU cc_start: 0.7910 (mp) cc_final: 0.7428 (pp) outliers start: 2 outliers final: 0 residues processed: 513 average time/residue: 0.4316 time to fit residues: 369.0663 Evaluate side-chains 408 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 0.0970 chunk 351 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 369 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 681 HIS ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 ASN ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35432 Z= 0.249 Angle : 0.775 13.227 48018 Z= 0.383 Chirality : 0.047 0.240 5620 Planarity : 0.004 0.052 5960 Dihedral : 6.516 30.980 4522 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.11 (0.12), residues: 4246 helix: -0.86 (0.12), residues: 1804 sheet: -2.01 (0.35), residues: 206 loop : -3.24 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 23 HIS 0.022 0.002 HIS A 543 PHE 0.025 0.002 PHE E 182 TYR 0.033 0.002 TYR F 30 ARG 0.005 0.001 ARG D 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6889 (pp30) cc_final: 0.6485 (pp30) REVERT: A 185 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8707 (pttp) REVERT: A 420 LEU cc_start: 0.8916 (tp) cc_final: 0.8536 (tp) REVERT: A 529 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6664 (pm20) REVERT: A 575 ASN cc_start: 0.8200 (m-40) cc_final: 0.7756 (p0) REVERT: A 576 ASN cc_start: 0.5587 (m110) cc_final: 0.4899 (m110) REVERT: A 628 LEU cc_start: 0.7466 (mm) cc_final: 0.6679 (pp) REVERT: A 743 MET cc_start: 0.4707 (tpt) cc_final: 0.4498 (ttp) REVERT: A 832 ASP cc_start: 0.8341 (m-30) cc_final: 0.8052 (t0) REVERT: B 28 MET cc_start: 0.8437 (mmt) cc_final: 0.7855 (mmp) REVERT: B 35 MET cc_start: 0.8371 (tmm) cc_final: 0.8038 (tmm) REVERT: B 37 MET cc_start: 0.8147 (tpp) cc_final: 0.7939 (tpp) REVERT: B 152 MET cc_start: 0.8504 (tpp) cc_final: 0.8144 (tpp) REVERT: B 204 PHE cc_start: 0.8025 (t80) cc_final: 0.7820 (t80) REVERT: B 471 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7666 (pttm) REVERT: B 478 MET cc_start: 0.6712 (tpt) cc_final: 0.6503 (tpt) REVERT: B 492 LEU cc_start: 0.8089 (mm) cc_final: 0.7871 (mm) REVERT: B 512 MET cc_start: 0.7587 (tpp) cc_final: 0.6920 (tpp) REVERT: C 149 ILE cc_start: 0.8994 (mm) cc_final: 0.8652 (tt) REVERT: C 458 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8516 (tm-30) REVERT: C 478 MET cc_start: 0.8332 (tmm) cc_final: 0.7947 (tmm) REVERT: C 484 ASP cc_start: 0.7875 (m-30) cc_final: 0.7263 (m-30) REVERT: C 511 GLN cc_start: 0.8621 (pt0) cc_final: 0.8026 (pp30) REVERT: C 567 LEU cc_start: 0.9349 (tt) cc_final: 0.8961 (tt) REVERT: D 19 ILE cc_start: 0.8589 (tp) cc_final: 0.8192 (mm) REVERT: D 185 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8573 (pttp) REVERT: D 420 LEU cc_start: 0.8899 (tp) cc_final: 0.8520 (tp) REVERT: D 628 LEU cc_start: 0.7534 (mm) cc_final: 0.6765 (pp) REVERT: D 743 MET cc_start: 0.4732 (tpt) cc_final: 0.4518 (ttp) REVERT: D 832 ASP cc_start: 0.8339 (m-30) cc_final: 0.8049 (t0) REVERT: E 6 GLU cc_start: 0.7725 (tp30) cc_final: 0.7118 (tp30) REVERT: E 28 MET cc_start: 0.8423 (mmp) cc_final: 0.7714 (mmp) REVERT: E 35 MET cc_start: 0.8392 (tmm) cc_final: 0.8060 (tmm) REVERT: E 37 MET cc_start: 0.8156 (tpp) cc_final: 0.7953 (tpp) REVERT: E 152 MET cc_start: 0.8501 (tpp) cc_final: 0.8202 (tpp) REVERT: E 204 PHE cc_start: 0.8053 (t80) cc_final: 0.7794 (t80) REVERT: E 471 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7722 (pttm) REVERT: E 478 MET cc_start: 0.6697 (tpt) cc_final: 0.6495 (tpt) REVERT: E 512 MET cc_start: 0.7374 (tpp) cc_final: 0.6673 (tpp) REVERT: E 578 MET cc_start: 0.5184 (mpp) cc_final: 0.4941 (mpp) REVERT: E 832 ASP cc_start: 0.7850 (p0) cc_final: 0.7608 (p0) REVERT: F 149 ILE cc_start: 0.8899 (mm) cc_final: 0.8609 (tt) REVERT: F 478 MET cc_start: 0.8202 (tmm) cc_final: 0.7902 (tmm) REVERT: F 484 ASP cc_start: 0.7834 (m-30) cc_final: 0.7515 (m-30) REVERT: F 511 GLN cc_start: 0.8628 (pt0) cc_final: 0.8072 (pp30) REVERT: F 548 ASP cc_start: 0.8231 (p0) cc_final: 0.7420 (p0) REVERT: F 567 LEU cc_start: 0.9360 (tt) cc_final: 0.9004 (tt) REVERT: F 634 MET cc_start: 0.7522 (mtt) cc_final: 0.6862 (mtt) REVERT: F 782 LEU cc_start: 0.7836 (mp) cc_final: 0.7309 (pp) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.4230 time to fit residues: 360.3188 Evaluate side-chains 375 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 10.0000 chunk 370 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 752 GLN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 796 GLN F 14 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35432 Z= 0.211 Angle : 0.768 13.638 48018 Z= 0.375 Chirality : 0.046 0.242 5620 Planarity : 0.004 0.049 5960 Dihedral : 6.305 30.305 4522 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.00 (0.12), residues: 4246 helix: -0.77 (0.12), residues: 1798 sheet: -1.79 (0.37), residues: 186 loop : -3.18 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 23 HIS 0.020 0.001 HIS A 543 PHE 0.033 0.002 PHE B 182 TYR 0.028 0.002 TYR F 30 ARG 0.005 0.001 ARG D 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6818 (pp30) cc_final: 0.6423 (pp30) REVERT: A 19 ILE cc_start: 0.8577 (tp) cc_final: 0.8359 (mm) REVERT: A 185 LYS cc_start: 0.9294 (mmmt) cc_final: 0.8783 (pttp) REVERT: A 372 ILE cc_start: 0.8913 (mm) cc_final: 0.8708 (tt) REVERT: A 420 LEU cc_start: 0.8717 (tp) cc_final: 0.8142 (tp) REVERT: A 512 MET cc_start: 0.6664 (mmm) cc_final: 0.6294 (tpp) REVERT: A 529 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6632 (pm20) REVERT: A 575 ASN cc_start: 0.8140 (m-40) cc_final: 0.7735 (p0) REVERT: A 576 ASN cc_start: 0.5373 (m110) cc_final: 0.4777 (m110) REVERT: A 628 LEU cc_start: 0.7350 (mm) cc_final: 0.6641 (pp) REVERT: B 35 MET cc_start: 0.8380 (tmm) cc_final: 0.8021 (tmm) REVERT: B 152 MET cc_start: 0.8477 (tpp) cc_final: 0.8139 (tpp) REVERT: B 204 PHE cc_start: 0.8056 (t80) cc_final: 0.7756 (t80) REVERT: B 471 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7593 (pttm) REVERT: B 492 LEU cc_start: 0.8098 (mm) cc_final: 0.7509 (mt) REVERT: B 512 MET cc_start: 0.7612 (tpp) cc_final: 0.6940 (tpp) REVERT: B 567 LEU cc_start: 0.8965 (tp) cc_final: 0.8678 (tp) REVERT: C 149 ILE cc_start: 0.8867 (mm) cc_final: 0.8667 (mm) REVERT: C 376 TYR cc_start: 0.9092 (t80) cc_final: 0.8851 (t80) REVERT: C 458 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8354 (tm-30) REVERT: C 478 MET cc_start: 0.8193 (tmm) cc_final: 0.7929 (tmm) REVERT: C 511 GLN cc_start: 0.8643 (pt0) cc_final: 0.8011 (pp30) REVERT: C 567 LEU cc_start: 0.9327 (tt) cc_final: 0.8873 (tt) REVERT: D 19 ILE cc_start: 0.8574 (tp) cc_final: 0.8334 (mm) REVERT: D 185 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8600 (pttp) REVERT: D 384 LEU cc_start: 0.8296 (mm) cc_final: 0.8062 (mm) REVERT: D 420 LEU cc_start: 0.8725 (tp) cc_final: 0.8125 (tp) REVERT: D 512 MET cc_start: 0.6508 (mmm) cc_final: 0.6200 (tpp) REVERT: D 628 LEU cc_start: 0.7505 (mm) cc_final: 0.6729 (pp) REVERT: E 28 MET cc_start: 0.8454 (mmp) cc_final: 0.8072 (mmp) REVERT: E 35 MET cc_start: 0.8382 (tmm) cc_final: 0.8013 (tmm) REVERT: E 152 MET cc_start: 0.8488 (tpp) cc_final: 0.8164 (tpp) REVERT: E 204 PHE cc_start: 0.8029 (t80) cc_final: 0.7753 (t80) REVERT: E 471 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7692 (pttm) REVERT: E 512 MET cc_start: 0.7450 (tpp) cc_final: 0.6969 (tpp) REVERT: E 567 LEU cc_start: 0.8994 (tp) cc_final: 0.8750 (tp) REVERT: E 578 MET cc_start: 0.5129 (mpp) cc_final: 0.4865 (mpp) REVERT: E 832 ASP cc_start: 0.7890 (p0) cc_final: 0.7663 (p0) REVERT: F 149 ILE cc_start: 0.8848 (mm) cc_final: 0.8621 (mm) REVERT: F 478 MET cc_start: 0.8110 (tmm) cc_final: 0.7889 (tmm) REVERT: F 511 GLN cc_start: 0.8581 (pt0) cc_final: 0.8028 (pp30) REVERT: F 548 ASP cc_start: 0.8229 (p0) cc_final: 0.7390 (p0) REVERT: F 567 LEU cc_start: 0.9341 (tt) cc_final: 0.8945 (tt) REVERT: F 634 MET cc_start: 0.7570 (mtt) cc_final: 0.6874 (mtt) REVERT: F 782 LEU cc_start: 0.7934 (mp) cc_final: 0.7653 (pp) REVERT: F 822 MET cc_start: 0.1955 (pmm) cc_final: 0.1431 (mtm) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.4345 time to fit residues: 368.7974 Evaluate side-chains 372 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 346 optimal weight: 0.0270 chunk 230 optimal weight: 0.9980 chunk 410 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN B 14 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 796 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35432 Z= 0.180 Angle : 0.771 14.030 48018 Z= 0.368 Chirality : 0.046 0.302 5620 Planarity : 0.004 0.048 5960 Dihedral : 6.100 28.542 4522 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.12), residues: 4246 helix: -0.70 (0.12), residues: 1808 sheet: -1.67 (0.36), residues: 186 loop : -3.12 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 208 HIS 0.013 0.001 HIS F 172 PHE 0.026 0.002 PHE D 321 TYR 0.022 0.002 TYR C 30 ARG 0.004 0.000 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7185 (pp30) cc_final: 0.6843 (pp30) REVERT: A 19 ILE cc_start: 0.8531 (tp) cc_final: 0.8224 (mm) REVERT: A 185 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8721 (pttp) REVERT: A 420 LEU cc_start: 0.8844 (tp) cc_final: 0.8256 (tp) REVERT: A 422 MET cc_start: 0.7599 (mtm) cc_final: 0.7154 (mtt) REVERT: A 478 MET cc_start: 0.6029 (tpt) cc_final: 0.5040 (ttt) REVERT: A 512 MET cc_start: 0.6747 (mmm) cc_final: 0.6224 (tpp) REVERT: A 529 GLN cc_start: 0.7281 (mm-40) cc_final: 0.6643 (pm20) REVERT: A 575 ASN cc_start: 0.8056 (m-40) cc_final: 0.7751 (p0) REVERT: A 576 ASN cc_start: 0.4833 (m110) cc_final: 0.4468 (m110) REVERT: A 628 LEU cc_start: 0.7326 (mm) cc_final: 0.6580 (pp) REVERT: B 6 GLU cc_start: 0.7881 (tp30) cc_final: 0.7459 (tp30) REVERT: B 35 MET cc_start: 0.8309 (tmm) cc_final: 0.7827 (tmm) REVERT: B 152 MET cc_start: 0.8276 (tpp) cc_final: 0.8025 (tpp) REVERT: B 373 ILE cc_start: 0.9457 (mm) cc_final: 0.8946 (tp) REVERT: B 471 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7546 (pttm) REVERT: B 492 LEU cc_start: 0.8043 (mm) cc_final: 0.7843 (mm) REVERT: B 512 MET cc_start: 0.7386 (tpp) cc_final: 0.7015 (tpp) REVERT: C 40 ILE cc_start: 0.9241 (mm) cc_final: 0.9006 (tp) REVERT: C 152 MET cc_start: 0.8364 (tpt) cc_final: 0.8134 (tpp) REVERT: C 376 TYR cc_start: 0.9081 (t80) cc_final: 0.8860 (t80) REVERT: C 422 MET cc_start: 0.8742 (tmm) cc_final: 0.8400 (tmm) REVERT: C 429 LEU cc_start: 0.7906 (tp) cc_final: 0.7643 (tp) REVERT: C 511 GLN cc_start: 0.8638 (pt0) cc_final: 0.8040 (pp30) REVERT: C 567 LEU cc_start: 0.9290 (tt) cc_final: 0.8836 (tt) REVERT: C 743 MET cc_start: 0.8014 (tmm) cc_final: 0.7379 (pmm) REVERT: D 11 ASN cc_start: 0.7466 (t0) cc_final: 0.7226 (t0) REVERT: D 19 ILE cc_start: 0.8463 (tp) cc_final: 0.8116 (mm) REVERT: D 185 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8632 (pttp) REVERT: D 420 LEU cc_start: 0.8860 (tp) cc_final: 0.8253 (tp) REVERT: D 422 MET cc_start: 0.7444 (mtm) cc_final: 0.7239 (mtt) REVERT: D 512 MET cc_start: 0.6621 (mmm) cc_final: 0.6175 (tpp) REVERT: D 546 PHE cc_start: 0.8234 (m-10) cc_final: 0.8001 (m-80) REVERT: D 628 LEU cc_start: 0.7447 (mm) cc_final: 0.6581 (pp) REVERT: D 632 LYS cc_start: 0.7543 (pttp) cc_final: 0.7308 (mmtt) REVERT: E 7 VAL cc_start: 0.9211 (m) cc_final: 0.8929 (p) REVERT: E 35 MET cc_start: 0.8315 (tmm) cc_final: 0.7850 (tmm) REVERT: E 152 MET cc_start: 0.8454 (tpp) cc_final: 0.8118 (tpp) REVERT: E 204 PHE cc_start: 0.8044 (t80) cc_final: 0.7808 (t80) REVERT: E 353 GLU cc_start: 0.7288 (tp30) cc_final: 0.7042 (tp30) REVERT: E 373 ILE cc_start: 0.9439 (mm) cc_final: 0.8906 (tp) REVERT: E 471 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7633 (pttm) REVERT: E 512 MET cc_start: 0.7190 (tpp) cc_final: 0.6901 (tpp) REVERT: E 578 MET cc_start: 0.5151 (mpp) cc_final: 0.4869 (mpp) REVERT: E 832 ASP cc_start: 0.7959 (p0) cc_final: 0.7712 (p0) REVERT: F 40 ILE cc_start: 0.9241 (mm) cc_final: 0.9011 (tp) REVERT: F 152 MET cc_start: 0.8384 (tpt) cc_final: 0.8147 (tpp) REVERT: F 511 GLN cc_start: 0.8623 (pt0) cc_final: 0.8016 (pp30) REVERT: F 548 ASP cc_start: 0.8224 (p0) cc_final: 0.7360 (p0) REVERT: F 567 LEU cc_start: 0.9303 (tt) cc_final: 0.8940 (tt) REVERT: F 634 MET cc_start: 0.7428 (mtt) cc_final: 0.6711 (mtt) REVERT: F 782 LEU cc_start: 0.7896 (mp) cc_final: 0.7670 (pp) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.4169 time to fit residues: 358.3223 Evaluate side-chains 375 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.0970 chunk 163 optimal weight: 0.0470 chunk 245 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 chunk 279 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 322 optimal weight: 5.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 421 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 HIS D 421 HIS D 576 ASN ** D 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35432 Z= 0.168 Angle : 0.763 10.795 48018 Z= 0.361 Chirality : 0.045 0.265 5620 Planarity : 0.004 0.051 5960 Dihedral : 5.831 28.000 4522 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.12), residues: 4246 helix: -0.69 (0.12), residues: 1830 sheet: -1.62 (0.36), residues: 186 loop : -3.13 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 208 HIS 0.012 0.001 HIS F 172 PHE 0.025 0.002 PHE E 182 TYR 0.018 0.002 TYR B 186 ARG 0.004 0.000 ARG E 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 4.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7223 (pp30) cc_final: 0.6771 (pp30) REVERT: A 19 ILE cc_start: 0.8382 (tp) cc_final: 0.8133 (mm) REVERT: A 20 LEU cc_start: 0.8924 (mt) cc_final: 0.8643 (mp) REVERT: A 185 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8780 (pttp) REVERT: A 420 LEU cc_start: 0.8989 (tp) cc_final: 0.8311 (tp) REVERT: A 422 MET cc_start: 0.7781 (mtm) cc_final: 0.7244 (mtt) REVERT: A 478 MET cc_start: 0.6006 (tpt) cc_final: 0.4999 (ttt) REVERT: A 529 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6781 (pm20) REVERT: A 545 LYS cc_start: 0.8318 (pttp) cc_final: 0.8017 (tmmt) REVERT: A 546 PHE cc_start: 0.8356 (m-10) cc_final: 0.7828 (m-80) REVERT: A 628 LEU cc_start: 0.7298 (mm) cc_final: 0.6520 (pp) REVERT: B 35 MET cc_start: 0.8275 (tmm) cc_final: 0.7693 (tmm) REVERT: B 152 MET cc_start: 0.8387 (tpp) cc_final: 0.8100 (tpp) REVERT: B 373 ILE cc_start: 0.9322 (mm) cc_final: 0.8833 (tp) REVERT: B 471 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7522 (pttm) REVERT: B 492 LEU cc_start: 0.7918 (mm) cc_final: 0.7712 (mm) REVERT: B 512 MET cc_start: 0.7525 (tpp) cc_final: 0.7307 (tpp) REVERT: C 152 MET cc_start: 0.8279 (tpt) cc_final: 0.8033 (tpp) REVERT: C 429 LEU cc_start: 0.7860 (tp) cc_final: 0.7594 (tp) REVERT: C 478 MET cc_start: 0.8154 (tmm) cc_final: 0.7890 (tmm) REVERT: C 511 GLN cc_start: 0.8530 (pt0) cc_final: 0.7990 (pp30) REVERT: C 567 LEU cc_start: 0.9270 (tt) cc_final: 0.8845 (tt) REVERT: D 11 ASN cc_start: 0.7659 (t0) cc_final: 0.7289 (t0) REVERT: D 19 ILE cc_start: 0.8445 (tp) cc_final: 0.8211 (mm) REVERT: D 185 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8597 (pttp) REVERT: D 420 LEU cc_start: 0.9002 (tp) cc_final: 0.8347 (tp) REVERT: D 422 MET cc_start: 0.7699 (mtm) cc_final: 0.7420 (mtt) REVERT: D 478 MET cc_start: 0.6005 (tpt) cc_final: 0.4950 (ttt) REVERT: D 628 LEU cc_start: 0.7478 (mm) cc_final: 0.6624 (pp) REVERT: D 632 LYS cc_start: 0.7429 (pttp) cc_final: 0.7154 (mmtt) REVERT: E 7 VAL cc_start: 0.9173 (m) cc_final: 0.8859 (p) REVERT: E 35 MET cc_start: 0.8312 (tmm) cc_final: 0.7808 (tmm) REVERT: E 152 MET cc_start: 0.8414 (tpp) cc_final: 0.8174 (tpp) REVERT: E 353 GLU cc_start: 0.7159 (tp30) cc_final: 0.6957 (tp30) REVERT: E 373 ILE cc_start: 0.9363 (mm) cc_final: 0.8868 (tp) REVERT: E 379 ILE cc_start: 0.8785 (tt) cc_final: 0.8575 (tt) REVERT: E 471 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7604 (pttm) REVERT: E 578 MET cc_start: 0.5086 (mpp) cc_final: 0.4781 (mpp) REVERT: E 832 ASP cc_start: 0.8017 (p0) cc_final: 0.7793 (p0) REVERT: F 149 ILE cc_start: 0.8743 (mm) cc_final: 0.8483 (tt) REVERT: F 152 MET cc_start: 0.8279 (tpt) cc_final: 0.8031 (tpp) REVERT: F 177 MET cc_start: 0.7463 (ttt) cc_final: 0.6731 (tmm) REVERT: F 478 MET cc_start: 0.8175 (tmm) cc_final: 0.7871 (tmm) REVERT: F 499 LEU cc_start: 0.8652 (tt) cc_final: 0.8439 (mt) REVERT: F 511 GLN cc_start: 0.8486 (pt0) cc_final: 0.7953 (pp30) REVERT: F 548 ASP cc_start: 0.8200 (p0) cc_final: 0.7326 (p0) REVERT: F 634 MET cc_start: 0.7403 (mtt) cc_final: 0.6718 (mtt) REVERT: F 743 MET cc_start: 0.7324 (tmm) cc_final: 0.7083 (pmm) REVERT: F 782 LEU cc_start: 0.7857 (mp) cc_final: 0.7644 (pp) REVERT: F 822 MET cc_start: 0.2535 (pmm) cc_final: 0.0709 (mtm) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.4241 time to fit residues: 389.7357 Evaluate side-chains 391 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 chunk 358 optimal weight: 0.9990 chunk 382 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 345 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 381 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35432 Z= 0.202 Angle : 0.783 13.052 48018 Z= 0.372 Chirality : 0.046 0.229 5620 Planarity : 0.004 0.057 5960 Dihedral : 5.827 26.706 4522 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.12), residues: 4246 helix: -0.70 (0.12), residues: 1854 sheet: -1.54 (0.36), residues: 186 loop : -3.16 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 386 HIS 0.013 0.001 HIS C 172 PHE 0.037 0.002 PHE E 329 TYR 0.027 0.002 TYR E 382 ARG 0.004 0.000 ARG D 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 489 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7174 (pp30) cc_final: 0.6698 (pp30) REVERT: A 20 LEU cc_start: 0.9014 (mt) cc_final: 0.8806 (mp) REVERT: A 185 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8795 (pttp) REVERT: A 205 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 478 MET cc_start: 0.6119 (tpt) cc_final: 0.5094 (ttt) REVERT: A 529 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6605 (pm20) REVERT: A 545 LYS cc_start: 0.8295 (pttp) cc_final: 0.7890 (tmmt) REVERT: A 546 PHE cc_start: 0.8191 (m-10) cc_final: 0.7787 (m-80) REVERT: A 628 LEU cc_start: 0.7370 (mm) cc_final: 0.6570 (pp) REVERT: B 35 MET cc_start: 0.8367 (tmm) cc_final: 0.7758 (tmm) REVERT: B 55 LEU cc_start: 0.8990 (pt) cc_final: 0.8679 (pt) REVERT: B 152 MET cc_start: 0.8498 (tpp) cc_final: 0.8202 (tpp) REVERT: B 373 ILE cc_start: 0.9409 (mm) cc_final: 0.8909 (tp) REVERT: B 471 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7658 (pttm) REVERT: B 567 LEU cc_start: 0.8672 (tp) cc_final: 0.8468 (tp) REVERT: C 177 MET cc_start: 0.7463 (ttt) cc_final: 0.7168 (ttt) REVERT: C 429 LEU cc_start: 0.7861 (tp) cc_final: 0.7589 (tp) REVERT: C 478 MET cc_start: 0.8192 (tmm) cc_final: 0.7934 (tmm) REVERT: C 511 GLN cc_start: 0.8654 (pt0) cc_final: 0.8125 (pp30) REVERT: C 567 LEU cc_start: 0.9312 (tt) cc_final: 0.8994 (tt) REVERT: D 11 ASN cc_start: 0.7677 (t0) cc_final: 0.7348 (t0) REVERT: D 179 SER cc_start: 0.8300 (t) cc_final: 0.8041 (p) REVERT: D 185 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8626 (pttp) REVERT: D 205 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8683 (mt-10) REVERT: D 478 MET cc_start: 0.6124 (tpt) cc_final: 0.5087 (ttt) REVERT: D 628 LEU cc_start: 0.7449 (mm) cc_final: 0.6588 (pp) REVERT: D 632 LYS cc_start: 0.7309 (pttp) cc_final: 0.6982 (mmtt) REVERT: E 7 VAL cc_start: 0.9403 (m) cc_final: 0.9124 (p) REVERT: E 35 MET cc_start: 0.8406 (tmm) cc_final: 0.7832 (tmm) REVERT: E 152 MET cc_start: 0.8501 (tpp) cc_final: 0.8195 (tpp) REVERT: E 353 GLU cc_start: 0.7401 (tp30) cc_final: 0.7133 (tp30) REVERT: E 373 ILE cc_start: 0.9434 (mm) cc_final: 0.8925 (tp) REVERT: E 471 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7608 (pttm) REVERT: E 832 ASP cc_start: 0.8073 (p0) cc_final: 0.7828 (p0) REVERT: F 149 ILE cc_start: 0.8769 (mm) cc_final: 0.8528 (tt) REVERT: F 177 MET cc_start: 0.7354 (ttt) cc_final: 0.7116 (ttt) REVERT: F 478 MET cc_start: 0.8103 (tmm) cc_final: 0.7803 (tmm) REVERT: F 511 GLN cc_start: 0.8533 (pt0) cc_final: 0.8028 (pp30) REVERT: F 548 ASP cc_start: 0.8087 (p0) cc_final: 0.7236 (p0) REVERT: F 634 MET cc_start: 0.7391 (mtt) cc_final: 0.6879 (mtt) REVERT: F 743 MET cc_start: 0.7420 (tmm) cc_final: 0.7183 (pmm) outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.4124 time to fit residues: 344.3944 Evaluate side-chains 367 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 8.9990 chunk 404 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 390 optimal weight: 0.5980 chunk 337 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 207 optimal weight: 0.0570 overall best weight: 3.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 796 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 35432 Z= 0.321 Angle : 0.869 12.747 48018 Z= 0.426 Chirality : 0.049 0.226 5620 Planarity : 0.005 0.054 5960 Dihedral : 6.323 28.745 4522 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.93 % Favored : 87.02 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.12), residues: 4246 helix: -0.97 (0.12), residues: 1856 sheet: -1.60 (0.37), residues: 176 loop : -3.15 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 386 HIS 0.012 0.002 HIS F 172 PHE 0.038 0.003 PHE B 329 TYR 0.037 0.003 TYR C 30 ARG 0.007 0.001 ARG E 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 4.498 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: A 14 GLN cc_start: 0.6715 (pp30) cc_final: 0.6513 (pp30) REVERT: A 179 SER cc_start: 0.8348 (t) cc_final: 0.8113 (p) REVERT: A 185 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8833 (pttp) REVERT: A 205 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 329 PHE cc_start: 0.8277 (p90) cc_final: 0.8050 (p90) REVERT: A 478 MET cc_start: 0.6248 (tpt) cc_final: 0.5256 (ttt) REVERT: A 628 LEU cc_start: 0.7381 (mm) cc_final: 0.6528 (pp) REVERT: B 35 MET cc_start: 0.8399 (tmm) cc_final: 0.8019 (tmm) REVERT: B 37 MET cc_start: 0.8176 (tpp) cc_final: 0.7869 (tmm) REVERT: B 55 LEU cc_start: 0.8948 (pt) cc_final: 0.8405 (pt) REVERT: B 152 MET cc_start: 0.8620 (tpp) cc_final: 0.8232 (tpp) REVERT: B 471 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7853 (pttm) REVERT: B 567 LEU cc_start: 0.8917 (tp) cc_final: 0.8677 (tp) REVERT: C 478 MET cc_start: 0.8258 (tmm) cc_final: 0.7813 (tmm) REVERT: C 511 GLN cc_start: 0.8858 (pt0) cc_final: 0.8260 (pp30) REVERT: D 14 GLN cc_start: 0.6942 (pp30) cc_final: 0.6695 (pp30) REVERT: D 185 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8786 (pttp) REVERT: D 329 PHE cc_start: 0.8301 (p90) cc_final: 0.8031 (p90) REVERT: D 358 MET cc_start: 0.8444 (mmm) cc_final: 0.8036 (mmp) REVERT: D 478 MET cc_start: 0.6374 (tpt) cc_final: 0.5302 (ttt) REVERT: D 512 MET cc_start: 0.7485 (mmm) cc_final: 0.6975 (tpp) REVERT: D 545 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8254 (tptt) REVERT: D 628 LEU cc_start: 0.7517 (mm) cc_final: 0.6653 (pp) REVERT: E 7 VAL cc_start: 0.9272 (m) cc_final: 0.8984 (p) REVERT: E 35 MET cc_start: 0.8483 (tmm) cc_final: 0.8176 (tmm) REVERT: E 152 MET cc_start: 0.8613 (tpp) cc_final: 0.8234 (tpp) REVERT: E 353 GLU cc_start: 0.7338 (tp30) cc_final: 0.6992 (tp30) REVERT: E 471 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7724 (pttm) REVERT: E 567 LEU cc_start: 0.8952 (tp) cc_final: 0.8751 (tp) REVERT: F 149 ILE cc_start: 0.8851 (mm) cc_final: 0.8603 (tt) REVERT: F 478 MET cc_start: 0.8201 (tmm) cc_final: 0.7876 (tmm) REVERT: F 511 GLN cc_start: 0.8712 (pt0) cc_final: 0.8178 (pp30) REVERT: F 548 ASP cc_start: 0.8150 (p0) cc_final: 0.7351 (p0) REVERT: F 567 LEU cc_start: 0.9407 (tt) cc_final: 0.9104 (tt) REVERT: F 634 MET cc_start: 0.7730 (mtt) cc_final: 0.7307 (mtt) REVERT: F 743 MET cc_start: 0.7434 (tmm) cc_final: 0.7154 (pmm) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.4095 time to fit residues: 312.3523 Evaluate side-chains 324 residues out of total 3994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.4980 chunk 360 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 141 optimal weight: 0.0470 chunk 347 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 594 HIS D 681 HIS ** D 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.119286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.091355 restraints weight = 115711.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093286 restraints weight = 69899.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.094616 restraints weight = 47666.539| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35432 Z= 0.198 Angle : 0.799 12.854 48018 Z= 0.384 Chirality : 0.047 0.207 5620 Planarity : 0.004 0.049 5960 Dihedral : 6.049 29.510 4522 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.12), residues: 4246 helix: -0.72 (0.12), residues: 1808 sheet: -1.67 (0.36), residues: 186 loop : -3.03 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 386 HIS 0.014 0.001 HIS F 589 PHE 0.028 0.002 PHE B 165 TYR 0.028 0.002 TYR E 382 ARG 0.005 0.000 ARG D 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7490.71 seconds wall clock time: 138 minutes 3.61 seconds (8283.61 seconds total)