Starting phenix.real_space_refine on Sun Aug 9 09:25:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.cif Found real_map, /net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29jf_57206/08_2026/29jf_57206.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 156 5.16 5 C 20788 2.51 5 N 5808 2.21 5 O 6294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33050 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8207 Classifications: {'peptide': 1022} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 956} Chain: "B" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8207 Classifications: {'peptide': 1022} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 956} Chain: "C" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8207 Classifications: {'peptide': 1022} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 956} Chain: "D" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8207 Classifications: {'peptide': 1022} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 956} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' MG': 1, 'YGX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' MG': 1, 'YGX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' MG': 1, 'YGX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' MG': 1, 'YGX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 6.07, per 1000 atoms: 0.18 Number of scatterers: 33050 At special positions: 0 Unit cell: (148.593, 191.302, 102.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 Mg 4 11.99 O 6294 8.00 N 5808 7.00 C 20788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 52 sheets defined 18.2% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 Processing helix chain 'A' and resid 6 through 13 removed outlier: 4.123A pdb=" N ARG A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.618A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.643A pdb=" N GLN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 136' Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.302A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.536A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.680A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.718A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.765A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.196A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.306A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 2 through 5 Processing helix chain 'B' and resid 6 through 13 removed outlier: 4.123A pdb=" N ARG B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.618A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.643A pdb=" N GLN B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.247A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.556A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.682A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.651A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.765A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 4.196A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.318A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 2 through 5 Processing helix chain 'C' and resid 6 through 13 removed outlier: 4.123A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.618A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.643A pdb=" N GLN C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.304A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.548A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.663A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.748A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.765A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 4.196A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.306A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 2 through 5 Processing helix chain 'D' and resid 6 through 13 removed outlier: 4.123A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.618A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 131 through 136 removed outlier: 3.643A pdb=" N GLN D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 136' Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.307A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.512A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.663A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.691A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.769A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 4.196A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.306A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.747A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.653A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.518A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 224 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 272 removed outlier: 5.438A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.087A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.739A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 723 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 696 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG A 721 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 698 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLN A 719 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A 700 " --> pdb=" O TRP A 717 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TRP A 717 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.371A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.370A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.284A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.257A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.747A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.653A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.518A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 224 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 272 removed outlier: 5.438A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.069A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.737A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 723 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 696 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG B 721 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 698 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B 719 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 700 " --> pdb=" O TRP B 717 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TRP B 717 " --> pdb=" O VAL B 700 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.371A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.370A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.284A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.257A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.747A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.653A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.518A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 224 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 272 removed outlier: 5.438A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.095A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.731A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 723 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 696 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG C 721 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 698 " --> pdb=" O GLN C 719 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN C 719 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 700 " --> pdb=" O TRP C 717 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TRP C 717 " --> pdb=" O VAL C 700 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.371A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.370A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.309A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.281A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.747A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.653A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.518A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 224 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 272 removed outlier: 5.438A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.098A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.731A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 723 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 696 " --> pdb=" O ARG D 721 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG D 721 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 698 " --> pdb=" O GLN D 719 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN D 719 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL D 700 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TRP D 717 " --> pdb=" O VAL D 700 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.371A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.370A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.315A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.279A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.251A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3132 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: 8.91 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5508 1.27 - 1.41: 8954 1.41 - 1.55: 19013 1.55 - 1.68: 121 1.68 - 1.82: 248 Bond restraints: 33844 Sorted by residual: bond pdb=" C VAL B 567 " pdb=" O VAL B 567 " ideal model delta sigma weight residual 1.239 1.128 0.111 1.22e-02 6.72e+03 8.32e+01 bond pdb=" C SER D 437 " pdb=" N GLU D 438 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.30e-02 5.92e+03 7.93e+01 bond pdb=" C SER C 437 " pdb=" N GLU C 438 " ideal model delta sigma weight residual 1.335 1.236 0.099 1.30e-02 5.92e+03 5.85e+01 bond pdb=" C MET D 502 " pdb=" O MET D 502 " ideal model delta sigma weight residual 1.236 1.166 0.069 1.17e-02 7.31e+03 3.52e+01 bond pdb=" C MET A 502 " pdb=" O MET A 502 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.17e-02 7.31e+03 3.40e+01 ... (remaining 33839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 34608 1.65 - 3.30: 9226 3.30 - 4.95: 1936 4.95 - 6.60: 358 6.60 - 8.24: 52 Bond angle restraints: 46180 Sorted by residual: angle pdb=" CA ASP C 859 " pdb=" CB ASP C 859 " pdb=" CG ASP C 859 " ideal model delta sigma weight residual 112.60 119.74 -7.14 1.00e+00 1.00e+00 5.10e+01 angle pdb=" CA ASP D 859 " pdb=" CB ASP D 859 " pdb=" CG ASP D 859 " ideal model delta sigma weight residual 112.60 119.74 -7.14 1.00e+00 1.00e+00 5.10e+01 angle pdb=" CA ASP A 859 " pdb=" CB ASP A 859 " pdb=" CG ASP A 859 " ideal model delta sigma weight residual 112.60 119.74 -7.14 1.00e+00 1.00e+00 5.09e+01 angle pdb=" CA ASP B 859 " pdb=" CB ASP B 859 " pdb=" CG ASP B 859 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.00e+00 1.00e+00 5.08e+01 angle pdb=" C ASN D 297 " pdb=" CA ASN D 297 " pdb=" CB ASN D 297 " ideal model delta sigma weight residual 111.20 115.85 -4.65 7.10e-01 1.98e+00 4.29e+01 ... (remaining 46175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18329 17.97 - 35.95: 1169 35.95 - 53.92: 229 53.92 - 71.89: 104 71.89 - 89.86: 61 Dihedral angle restraints: 19892 sinusoidal: 8076 harmonic: 11816 Sorted by residual: dihedral pdb=" CA ASP D 746 " pdb=" C ASP D 746 " pdb=" N PHE D 747 " pdb=" CA PHE D 747 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASP C 746 " pdb=" C ASP C 746 " pdb=" N PHE C 747 " pdb=" CA PHE C 747 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASP A 746 " pdb=" C ASP A 746 " pdb=" N PHE A 747 " pdb=" CA PHE A 747 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 19889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2938 0.081 - 0.161: 1530 0.161 - 0.242: 281 0.242 - 0.322: 61 0.322 - 0.403: 30 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ARG A 611 " pdb=" N ARG A 611 " pdb=" C ARG A 611 " pdb=" CB ARG A 611 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA ARG C 611 " pdb=" N ARG C 611 " pdb=" C ARG C 611 " pdb=" CB ARG C 611 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA ARG B 611 " pdb=" N ARG B 611 " pdb=" C ARG B 611 " pdb=" CB ARG B 611 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 4837 not shown) Planarity restraints: 6092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 568 " 0.140 2.00e-02 2.50e+03 6.75e-02 1.14e+02 pdb=" CG TRP B 568 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 568 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 568 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP B 568 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP B 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 568 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 568 " 0.070 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 568 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP B 568 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 695 " -0.113 2.00e-02 2.50e+03 6.48e-02 1.05e+02 pdb=" CG TRP B 695 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP B 695 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 695 " 0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP B 695 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP B 695 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 695 " 0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 695 " -0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 695 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 695 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 695 " 0.115 2.00e-02 2.50e+03 6.42e-02 1.03e+02 pdb=" CG TRP A 695 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 695 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 695 " -0.067 2.00e-02 2.50e+03 pdb=" NE1 TRP A 695 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP A 695 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 695 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 695 " 0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 695 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 695 " 0.080 2.00e-02 2.50e+03 ... (remaining 6089 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 128 2.57 - 3.15: 25349 3.15 - 3.73: 54718 3.73 - 4.32: 84269 4.32 - 4.90: 133275 Nonbonded interactions: 297739 Sorted by model distance: nonbonded pdb=" OE1 GLU B 461 " pdb="MG MG B1101 " model vdw 1.983 2.170 nonbonded pdb=" OE1 GLU D 461 " pdb="MG MG D1101 " model vdw 1.984 2.170 nonbonded pdb=" OE1 GLU C 461 " pdb="MG MG C1101 " model vdw 1.984 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1205 " model vdw 1.999 2.170 nonbonded pdb="MG MG B1101 " pdb=" O HOH B1205 " model vdw 2.023 2.170 ... (remaining 297734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.460 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: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.011 0.116 33848 Z= 0.682 Angle : 1.584 8.245 46180 Z= 1.047 Chirality : 0.096 0.403 4840 Planarity : 0.016 0.264 6092 Dihedral : 14.527 89.860 12284 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4080 helix: -2.38 (0.18), residues: 528 sheet: 0.16 (0.14), residues: 1148 loop : -0.68 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.003 ARG B 13 TYR 0.107 0.015 TYR A 559 PHE 0.055 0.011 PHE A 235 TRP 0.140 0.018 TRP B 568 HIS 0.022 0.004 HIS D 622 Details of bonding type rmsd/Z covalent geometry : bond 0.01056 / 0.68 (33844) covalent geometry : angle 1.58427 / 1.05 (46180) hydrogen bonds : bond 0.15067 / 9.89 ( 1172) hydrogen bonds : angle 7.79633 / 5.46 ( 3132) Misc. bond : bond 0.05882 / 2.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.5956 (tpp) cc_final: 0.5674 (tpt) REVERT: A 12 GLN cc_start: 0.7455 (tp40) cc_final: 0.7239 (tp40) REVERT: A 130 ASP cc_start: 0.6281 (p0) cc_final: 0.6014 (p0) REVERT: A 219 THR cc_start: 0.7891 (m) cc_final: 0.7588 (p) REVERT: A 255 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7680 (mmt-90) REVERT: A 274 PHE cc_start: 0.7535 (m-80) cc_final: 0.7035 (m-80) REVERT: A 655 MET cc_start: 0.7051 (ttm) cc_final: 0.6744 (tmm) REVERT: A 746 ASP cc_start: 0.6386 (p0) cc_final: 0.5964 (m-30) REVERT: A 753 ASN cc_start: 0.7224 (p0) cc_final: 0.6944 (p0) REVERT: A 804 ASN cc_start: 0.6980 (t0) cc_final: 0.6748 (t0) REVERT: A 977 HIS cc_start: 0.7546 (p-80) cc_final: 0.7275 (p-80) REVERT: B 2 MET cc_start: 0.5953 (tpp) cc_final: 0.5670 (tpt) REVERT: B 12 GLN cc_start: 0.7454 (tp40) cc_final: 0.7240 (tp40) REVERT: B 130 ASP cc_start: 0.6283 (p0) cc_final: 0.6015 (p0) REVERT: B 219 THR cc_start: 0.7889 (m) cc_final: 0.7585 (p) REVERT: B 255 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7683 (mmt-90) REVERT: B 274 PHE cc_start: 0.7543 (m-80) cc_final: 0.7039 (m-80) REVERT: B 277 GLU cc_start: 0.7090 (pm20) cc_final: 0.6869 (pp20) REVERT: B 655 MET cc_start: 0.7053 (ttm) cc_final: 0.6747 (tmm) REVERT: B 746 ASP cc_start: 0.6386 (p0) cc_final: 0.5966 (m-30) REVERT: B 753 ASN cc_start: 0.7225 (p0) cc_final: 0.6945 (p0) REVERT: B 804 ASN cc_start: 0.6982 (t0) cc_final: 0.6748 (t0) REVERT: B 977 HIS cc_start: 0.7549 (p-80) cc_final: 0.7278 (p-80) REVERT: C 2 MET cc_start: 0.5953 (tpp) cc_final: 0.5673 (tpt) REVERT: C 12 GLN cc_start: 0.7454 (tp40) cc_final: 0.7242 (tp40) REVERT: C 130 ASP cc_start: 0.6283 (p0) cc_final: 0.6016 (p0) REVERT: C 219 THR cc_start: 0.7889 (m) cc_final: 0.7584 (p) REVERT: C 255 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7677 (mmt-90) REVERT: C 274 PHE cc_start: 0.7500 (m-80) cc_final: 0.6937 (m-80) REVERT: C 338 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7459 (tp30) REVERT: C 655 MET cc_start: 0.7062 (ttm) cc_final: 0.6762 (tmm) REVERT: C 746 ASP cc_start: 0.6403 (p0) cc_final: 0.5979 (m-30) REVERT: C 753 ASN cc_start: 0.7222 (p0) cc_final: 0.6946 (p0) REVERT: C 804 ASN cc_start: 0.6980 (t0) cc_final: 0.6749 (t0) REVERT: C 977 HIS cc_start: 0.7547 (p-80) cc_final: 0.7274 (p-80) REVERT: D 2 MET cc_start: 0.5955 (tpp) cc_final: 0.5673 (tpt) REVERT: D 12 GLN cc_start: 0.7454 (tp40) cc_final: 0.7243 (tp40) REVERT: D 130 ASP cc_start: 0.6284 (p0) cc_final: 0.6018 (p0) REVERT: D 219 THR cc_start: 0.7889 (m) cc_final: 0.7586 (p) REVERT: D 255 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7680 (mmt-90) REVERT: D 274 PHE cc_start: 0.7499 (m-80) cc_final: 0.6938 (m-80) REVERT: D 277 GLU cc_start: 0.6984 (pm20) cc_final: 0.6777 (pp20) REVERT: D 338 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7454 (tp30) REVERT: D 655 MET cc_start: 0.7059 (ttm) cc_final: 0.6760 (tmm) REVERT: D 746 ASP cc_start: 0.6405 (p0) cc_final: 0.5982 (m-30) REVERT: D 753 ASN cc_start: 0.7223 (p0) cc_final: 0.6946 (p0) REVERT: D 804 ASN cc_start: 0.6981 (t0) cc_final: 0.6749 (t0) REVERT: D 977 HIS cc_start: 0.7547 (p-80) cc_final: 0.7277 (p-80) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.8364 time to fit residues: 419.3105 Evaluate side-chains 263 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 245 GLN A 339 ASN A 540 HIS A 624 GLN A 628 GLN A 675 GLN A 702 GLN A 844 HIS B 49 GLN B 245 GLN B 262 GLN B 339 ASN B 624 GLN B 628 GLN B 702 GLN B 844 HIS C 49 GLN C 245 GLN C 540 HIS C 624 GLN C 628 GLN C 702 GLN C 718 GLN C 844 HIS D 49 GLN D 245 GLN D 339 ASN D 540 HIS D 624 GLN D 628 GLN D 702 GLN D 718 GLN D 844 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065609 restraints weight = 66629.265| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.94 r_work: 0.3003 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33848 Z= 0.124 Angle : 0.592 6.428 46180 Z= 0.321 Chirality : 0.046 0.156 4840 Planarity : 0.004 0.051 6092 Dihedral : 5.942 27.985 4564 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 9.55 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4080 helix: -0.88 (0.20), residues: 540 sheet: -0.01 (0.13), residues: 1360 loop : -0.02 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 52 TYR 0.016 0.002 TYR D 503 PHE 0.020 0.002 PHE B 549 TRP 0.041 0.002 TRP D 553 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (33844) covalent geometry : angle 0.59216 / 0.32 (46180) hydrogen bonds : bond 0.04258 / 2.80 ( 1172) hydrogen bonds : angle 5.86423 / 4.13 ( 3132) Misc. bond : bond 0.00076 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 1.026 Fit side-chains REVERT: A 230 ARG cc_start: 0.7933 (mpt90) cc_final: 0.7674 (mpt-90) REVERT: A 251 ARG cc_start: 0.6087 (mmm-85) cc_final: 0.5770 (mmp-170) REVERT: A 274 PHE cc_start: 0.7525 (m-80) cc_final: 0.6939 (m-80) REVERT: A 277 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6176 (pp20) REVERT: A 280 ASP cc_start: 0.6622 (m-30) cc_final: 0.6411 (m-30) REVERT: A 515 VAL cc_start: 0.6721 (OUTLIER) cc_final: 0.6495 (t) REVERT: A 655 MET cc_start: 0.7308 (ttm) cc_final: 0.6962 (tmm) REVERT: A 746 ASP cc_start: 0.6643 (p0) cc_final: 0.6086 (m-30) REVERT: A 753 ASN cc_start: 0.7347 (p0) cc_final: 0.6877 (p0) REVERT: A 768 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6885 (tmm) REVERT: A 977 HIS cc_start: 0.7274 (p-80) cc_final: 0.6970 (p90) REVERT: A 999 TRP cc_start: 0.6667 (p90) cc_final: 0.6368 (p90) REVERT: B 230 ARG cc_start: 0.7954 (mpt90) cc_final: 0.7695 (mpt-90) REVERT: B 251 ARG cc_start: 0.6079 (mmm-85) cc_final: 0.5759 (mmp-170) REVERT: B 274 PHE cc_start: 0.7516 (m-80) cc_final: 0.6956 (m-80) REVERT: B 288 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7132 (mtt90) REVERT: B 502 MET cc_start: 0.8182 (mtm) cc_final: 0.7922 (mtt) REVERT: B 515 VAL cc_start: 0.6729 (OUTLIER) cc_final: 0.6509 (t) REVERT: B 655 MET cc_start: 0.7323 (ttm) cc_final: 0.6964 (tmm) REVERT: B 746 ASP cc_start: 0.6638 (p0) cc_final: 0.6072 (m-30) REVERT: B 753 ASN cc_start: 0.7366 (p0) cc_final: 0.6898 (p0) REVERT: B 768 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6879 (tmm) REVERT: B 977 HIS cc_start: 0.7273 (p-80) cc_final: 0.6970 (p90) REVERT: C 230 ARG cc_start: 0.7948 (mpt90) cc_final: 0.7688 (mpt-90) REVERT: C 251 ARG cc_start: 0.6105 (mmm-85) cc_final: 0.5788 (mmp-170) REVERT: C 274 PHE cc_start: 0.7528 (m-80) cc_final: 0.6963 (m-80) REVERT: C 277 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5885 (pp20) REVERT: C 338 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7348 (mm-30) REVERT: C 507 ASP cc_start: 0.6946 (m-30) cc_final: 0.6546 (m-30) REVERT: C 515 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6496 (t) REVERT: C 655 MET cc_start: 0.7288 (ttm) cc_final: 0.6933 (tmm) REVERT: C 753 ASN cc_start: 0.7362 (p0) cc_final: 0.6896 (p0) REVERT: C 768 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6900 (tmm) REVERT: C 977 HIS cc_start: 0.7274 (p-80) cc_final: 0.6970 (p90) REVERT: C 999 TRP cc_start: 0.6656 (p90) cc_final: 0.6355 (p90) REVERT: C 1013 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: D 230 ARG cc_start: 0.7911 (mpt90) cc_final: 0.7654 (mpt-90) REVERT: D 233 ASP cc_start: 0.7032 (p0) cc_final: 0.6820 (p0) REVERT: D 251 ARG cc_start: 0.6095 (mmm-85) cc_final: 0.5768 (mmp-170) REVERT: D 274 PHE cc_start: 0.7548 (m-80) cc_final: 0.6937 (m-80) REVERT: D 280 ASP cc_start: 0.6643 (m-30) cc_final: 0.6409 (m-30) REVERT: D 338 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7330 (mm-30) REVERT: D 515 VAL cc_start: 0.6685 (OUTLIER) cc_final: 0.6478 (t) REVERT: D 655 MET cc_start: 0.7298 (ttm) cc_final: 0.6941 (tmm) REVERT: D 746 ASP cc_start: 0.6761 (p0) cc_final: 0.6156 (m-30) REVERT: D 753 ASN cc_start: 0.7349 (p0) cc_final: 0.6880 (p0) REVERT: D 768 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6884 (tmm) REVERT: D 977 HIS cc_start: 0.7265 (p-80) cc_final: 0.6962 (p90) REVERT: D 999 TRP cc_start: 0.6657 (p90) cc_final: 0.6357 (p90) outliers start: 39 outliers final: 0 residues processed: 299 average time/residue: 0.7726 time to fit residues: 268.3420 Evaluate side-chains 242 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 232 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 768 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 242 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 161 optimal weight: 0.1980 chunk 354 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 266 GLN A 339 ASN A 363 HIS A 468 HIS A 583 ASN A 623 GLN A 761 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN B 339 ASN B 363 HIS B 468 HIS B 540 HIS B 583 ASN B 623 GLN B 761 GLN B1015 HIS C 266 GLN C 363 HIS C 394 ASN C 468 HIS C 583 ASN C 623 GLN C1015 HIS D 266 GLN D 339 ASN D 363 HIS D 468 HIS D 583 ASN D 623 GLN D1015 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065137 restraints weight = 67478.763| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.92 r_work: 0.2996 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 33848 Z= 0.255 Angle : 0.692 7.803 46180 Z= 0.363 Chirality : 0.049 0.169 4840 Planarity : 0.006 0.066 6092 Dihedral : 5.870 28.009 4564 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.06 % Allowed : 10.30 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4080 helix: -1.20 (0.19), residues: 540 sheet: -0.21 (0.13), residues: 1384 loop : -0.09 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1013 TYR 0.021 0.003 TYR C 856 PHE 0.016 0.003 PHE D 989 TRP 0.035 0.003 TRP C 553 HIS 0.005 0.002 HIS B 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (33844) covalent geometry : angle 0.69180 / 0.36 (46180) hydrogen bonds : bond 0.04348 / 2.91 ( 1172) hydrogen bonds : angle 5.95431 / 4.19 ( 3132) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 1.225 Fit side-chains REVERT: A 136 GLU cc_start: 0.6545 (pp20) cc_final: 0.6258 (pp20) REVERT: A 274 PHE cc_start: 0.7585 (m-80) cc_final: 0.6999 (m-80) REVERT: A 277 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6110 (pp20) REVERT: A 546 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 635 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7572 (p) REVERT: A 655 MET cc_start: 0.7230 (ttm) cc_final: 0.6837 (tmm) REVERT: A 768 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6851 (tmm) REVERT: A 977 HIS cc_start: 0.7241 (p-80) cc_final: 0.6966 (p-80) REVERT: B 136 GLU cc_start: 0.6545 (pp20) cc_final: 0.6263 (pp20) REVERT: B 274 PHE cc_start: 0.7569 (m-80) cc_final: 0.6985 (m-80) REVERT: B 502 MET cc_start: 0.8286 (mtm) cc_final: 0.8033 (mtt) REVERT: B 635 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 655 MET cc_start: 0.7193 (ttm) cc_final: 0.6792 (tmm) REVERT: B 768 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6857 (tmm) REVERT: B 977 HIS cc_start: 0.7229 (p-80) cc_final: 0.6953 (p-80) REVERT: C 136 GLU cc_start: 0.6531 (pp20) cc_final: 0.6252 (pp20) REVERT: C 274 PHE cc_start: 0.7575 (m-80) cc_final: 0.7027 (m-80) REVERT: C 277 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5910 (pp20) REVERT: C 502 MET cc_start: 0.8245 (mtm) cc_final: 0.8008 (mtp) REVERT: C 546 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 635 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7598 (p) REVERT: C 655 MET cc_start: 0.7191 (ttm) cc_final: 0.6796 (tmm) REVERT: C 768 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6835 (tmm) REVERT: C 977 HIS cc_start: 0.7244 (p-80) cc_final: 0.6970 (p-80) REVERT: D 136 GLU cc_start: 0.6546 (pp20) cc_final: 0.6263 (pp20) REVERT: D 274 PHE cc_start: 0.7575 (m-80) cc_final: 0.7036 (m-80) REVERT: D 546 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8093 (tp) REVERT: D 635 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 655 MET cc_start: 0.7192 (ttm) cc_final: 0.6801 (tmm) REVERT: D 768 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6840 (tmm) REVERT: D 977 HIS cc_start: 0.7239 (p-80) cc_final: 0.6965 (p-80) outliers start: 72 outliers final: 19 residues processed: 291 average time/residue: 0.7935 time to fit residues: 267.5307 Evaluate side-chains 244 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 891 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 379 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 308 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 761 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 761 GLN C 761 GLN D 339 ASN D 761 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066482 restraints weight = 66911.204| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.93 r_work: 0.3027 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33848 Z= 0.140 Angle : 0.551 6.501 46180 Z= 0.291 Chirality : 0.044 0.149 4840 Planarity : 0.004 0.036 6092 Dihedral : 5.295 23.247 4564 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.54 % Allowed : 12.01 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4080 helix: -0.77 (0.20), residues: 544 sheet: -0.15 (0.14), residues: 1360 loop : 0.01 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1013 TYR 0.016 0.002 TYR A 100 PHE 0.015 0.001 PHE B 549 TRP 0.031 0.002 TRP C 553 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (33844) covalent geometry : angle 0.55063 / 0.29 (46180) hydrogen bonds : bond 0.03497 / 2.32 ( 1172) hydrogen bonds : angle 5.53299 / 3.89 ( 3132) Misc. bond : bond 0.00033 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 1.138 Fit side-chains REVERT: A 136 GLU cc_start: 0.6540 (pp20) cc_final: 0.6231 (pp20) REVERT: A 237 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6964 (mtp-110) REVERT: A 251 ARG cc_start: 0.6256 (mmm-85) cc_final: 0.5849 (mmp-170) REVERT: A 274 PHE cc_start: 0.7526 (m-80) cc_final: 0.6963 (m-80) REVERT: A 277 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5993 (pp20) REVERT: A 280 ASP cc_start: 0.6642 (m-30) cc_final: 0.6368 (m-30) REVERT: A 635 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 655 MET cc_start: 0.7178 (ttm) cc_final: 0.6847 (tmm) REVERT: A 768 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6803 (tmm) REVERT: A 977 HIS cc_start: 0.7255 (p-80) cc_final: 0.6964 (p-80) REVERT: B 136 GLU cc_start: 0.6547 (pp20) cc_final: 0.6240 (pp20) REVERT: B 237 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6992 (mtp-110) REVERT: B 251 ARG cc_start: 0.6273 (mmm-85) cc_final: 0.5871 (mmp-170) REVERT: B 274 PHE cc_start: 0.7506 (m-80) cc_final: 0.6959 (m-80) REVERT: B 502 MET cc_start: 0.8183 (mtm) cc_final: 0.7927 (mtt) REVERT: B 546 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 635 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (p) REVERT: B 655 MET cc_start: 0.7133 (ttm) cc_final: 0.6823 (tmm) REVERT: B 768 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6822 (tmm) REVERT: B 977 HIS cc_start: 0.7254 (p-80) cc_final: 0.6964 (p-80) REVERT: C 136 GLU cc_start: 0.6547 (pp20) cc_final: 0.6240 (pp20) REVERT: C 237 ARG cc_start: 0.7301 (mtp85) cc_final: 0.7022 (mtp-110) REVERT: C 274 PHE cc_start: 0.7489 (m-80) cc_final: 0.6914 (m-80) REVERT: C 277 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: C 339 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7251 (m110) REVERT: C 635 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7496 (p) REVERT: C 655 MET cc_start: 0.7154 (ttm) cc_final: 0.6832 (tmm) REVERT: C 768 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: C 977 HIS cc_start: 0.7239 (p-80) cc_final: 0.6949 (p-80) REVERT: D 136 GLU cc_start: 0.6551 (pp20) cc_final: 0.6247 (pp20) REVERT: D 237 ARG cc_start: 0.7291 (mtp85) cc_final: 0.7013 (mtp-110) REVERT: D 251 ARG cc_start: 0.6284 (mmm-85) cc_final: 0.5885 (mmp-170) REVERT: D 274 PHE cc_start: 0.7485 (m-80) cc_final: 0.6928 (m-80) REVERT: D 280 ASP cc_start: 0.6720 (m-30) cc_final: 0.6414 (m-30) REVERT: D 635 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7498 (p) REVERT: D 655 MET cc_start: 0.7156 (ttm) cc_final: 0.6842 (tmm) REVERT: D 768 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6838 (tmm) REVERT: D 977 HIS cc_start: 0.7258 (p-80) cc_final: 0.6967 (p-80) outliers start: 54 outliers final: 16 residues processed: 267 average time/residue: 0.8811 time to fit residues: 271.3015 Evaluate side-chains 246 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 768 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 0.0040 chunk 161 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN C 761 GLN D 675 GLN D 761 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.078265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066498 restraints weight = 67160.712| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.93 r_work: 0.3031 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33848 Z= 0.180 Angle : 0.579 6.595 46180 Z= 0.305 Chirality : 0.045 0.157 4840 Planarity : 0.005 0.038 6092 Dihedral : 5.308 22.159 4564 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.80 % Allowed : 11.96 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4080 helix: -0.51 (0.21), residues: 520 sheet: -0.18 (0.14), residues: 1360 loop : -0.02 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1013 TYR 0.017 0.002 TYR D 856 PHE 0.013 0.002 PHE D 989 TRP 0.027 0.002 TRP C 553 HIS 0.005 0.001 HIS C 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (33844) covalent geometry : angle 0.57905 / 0.30 (46180) hydrogen bonds : bond 0.03615 / 2.42 ( 1172) hydrogen bonds : angle 5.58877 / 3.93 ( 3132) Misc. bond : bond 0.00018 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 226 time to evaluate : 1.015 Fit side-chains REVERT: A 136 GLU cc_start: 0.6510 (pp20) cc_final: 0.6295 (pp20) REVERT: A 274 PHE cc_start: 0.7512 (m-80) cc_final: 0.6973 (m-80) REVERT: A 277 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5844 (pp20) REVERT: A 280 ASP cc_start: 0.6655 (m-30) cc_final: 0.6331 (m-30) REVERT: A 546 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8144 (tp) REVERT: A 635 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 655 MET cc_start: 0.7119 (ttm) cc_final: 0.6793 (tmm) REVERT: A 768 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6687 (tmm) REVERT: A 977 HIS cc_start: 0.7279 (p-80) cc_final: 0.7011 (p-80) REVERT: B 136 GLU cc_start: 0.6494 (pp20) cc_final: 0.6284 (pp20) REVERT: B 274 PHE cc_start: 0.7495 (m-80) cc_final: 0.6965 (m-80) REVERT: B 502 MET cc_start: 0.8229 (mtm) cc_final: 0.7968 (mtt) REVERT: B 546 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 635 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7468 (p) REVERT: B 655 MET cc_start: 0.7123 (ttm) cc_final: 0.6801 (tmm) REVERT: B 768 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6688 (tmm) REVERT: B 977 HIS cc_start: 0.7265 (p-80) cc_final: 0.6998 (p-80) REVERT: C 136 GLU cc_start: 0.6497 (pp20) cc_final: 0.6286 (pp20) REVERT: C 237 ARG cc_start: 0.7307 (mtp85) cc_final: 0.7058 (mtp-110) REVERT: C 274 PHE cc_start: 0.7468 (m-80) cc_final: 0.6943 (m-80) REVERT: C 277 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5849 (pp20) REVERT: C 339 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7290 (m110) REVERT: C 546 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8138 (tp) REVERT: C 635 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7553 (p) REVERT: C 655 MET cc_start: 0.7147 (ttm) cc_final: 0.6819 (tmm) REVERT: C 768 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6693 (tmm) REVERT: C 977 HIS cc_start: 0.7261 (p-80) cc_final: 0.6996 (p-80) REVERT: D 136 GLU cc_start: 0.6507 (pp20) cc_final: 0.6296 (pp20) REVERT: D 237 ARG cc_start: 0.7300 (mtp85) cc_final: 0.7050 (mtp-110) REVERT: D 280 ASP cc_start: 0.6681 (m-30) cc_final: 0.6365 (m-30) REVERT: D 546 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8154 (tp) REVERT: D 635 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7505 (p) REVERT: D 655 MET cc_start: 0.7151 (ttm) cc_final: 0.6827 (tmm) REVERT: D 768 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6680 (tmm) REVERT: D 977 HIS cc_start: 0.7278 (p-80) cc_final: 0.7012 (p-80) outliers start: 63 outliers final: 30 residues processed: 271 average time/residue: 0.8345 time to fit residues: 261.8082 Evaluate side-chains 262 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 891 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 169 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 350 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 675 GLN C 394 ASN C 761 GLN D 339 ASN D 394 ASN D 761 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.078037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066242 restraints weight = 66911.745| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.92 r_work: 0.3027 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33848 Z= 0.244 Angle : 0.646 7.393 46180 Z= 0.340 Chirality : 0.048 0.173 4840 Planarity : 0.005 0.052 6092 Dihedral : 5.589 22.426 4564 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.92 % Allowed : 12.39 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4080 helix: -0.90 (0.20), residues: 516 sheet: -0.34 (0.14), residues: 1360 loop : -0.10 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1013 TYR 0.019 0.003 TYR C 856 PHE 0.018 0.002 PHE D 989 TRP 0.028 0.002 TRP A 553 HIS 0.009 0.002 HIS C 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 (33844) covalent geometry : angle 0.64574 / 0.34 (46180) hydrogen bonds : bond 0.03969 / 2.67 ( 1172) hydrogen bonds : angle 5.80624 / 4.08 ( 3132) Misc. bond : bond 0.00051 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 1.280 Fit side-chains REVERT: A 144 ASP cc_start: 0.7372 (m-30) cc_final: 0.7102 (m-30) REVERT: A 274 PHE cc_start: 0.7509 (m-80) cc_final: 0.6988 (m-80) REVERT: A 277 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5995 (pp20) REVERT: A 280 ASP cc_start: 0.6689 (m-30) cc_final: 0.6330 (m-30) REVERT: A 546 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8156 (tp) REVERT: A 635 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7525 (p) REVERT: A 655 MET cc_start: 0.7252 (ttm) cc_final: 0.6905 (tmm) REVERT: A 768 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6764 (tmm) REVERT: A 977 HIS cc_start: 0.7252 (p-80) cc_final: 0.7031 (p-80) REVERT: B 274 PHE cc_start: 0.7494 (m-80) cc_final: 0.6947 (m-80) REVERT: B 546 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 635 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7507 (p) REVERT: B 655 MET cc_start: 0.7230 (ttm) cc_final: 0.6887 (tmm) REVERT: B 768 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6773 (tmm) REVERT: B 977 HIS cc_start: 0.7240 (p-80) cc_final: 0.7020 (p-80) REVERT: C 144 ASP cc_start: 0.7388 (m-30) cc_final: 0.7115 (m-30) REVERT: C 274 PHE cc_start: 0.7485 (m-80) cc_final: 0.6985 (m-80) REVERT: C 277 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5841 (pp20) REVERT: C 546 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 635 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (p) REVERT: C 655 MET cc_start: 0.7265 (ttm) cc_final: 0.6916 (tmm) REVERT: C 768 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6773 (tmm) REVERT: C 977 HIS cc_start: 0.7251 (p-80) cc_final: 0.7033 (p-80) REVERT: D 280 ASP cc_start: 0.6645 (m-30) cc_final: 0.6319 (m-30) REVERT: D 338 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7284 (mm-30) REVERT: D 546 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8123 (tp) REVERT: D 635 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7542 (p) REVERT: D 655 MET cc_start: 0.7276 (ttm) cc_final: 0.6929 (tmm) REVERT: D 768 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6774 (tmm) REVERT: D 977 HIS cc_start: 0.7254 (p-80) cc_final: 0.7033 (p-80) outliers start: 67 outliers final: 33 residues processed: 283 average time/residue: 0.7734 time to fit residues: 254.2656 Evaluate side-chains 271 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 891 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 365 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 396 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS A 394 ASN A 624 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 775 GLN C 216 HIS C 394 ASN C 624 GLN D 394 ASN D 624 GLN D 775 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067802 restraints weight = 66943.648| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.94 r_work: 0.3062 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33848 Z= 0.114 Angle : 0.520 6.270 46180 Z= 0.274 Chirality : 0.043 0.141 4840 Planarity : 0.004 0.042 6092 Dihedral : 5.011 20.214 4564 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.40 % Allowed : 12.87 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4080 helix: -0.22 (0.22), residues: 520 sheet: -0.21 (0.14), residues: 1368 loop : 0.04 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1013 TYR 0.015 0.002 TYR C 100 PHE 0.011 0.001 PHE A 747 TRP 0.031 0.002 TRP A 553 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (33844) covalent geometry : angle 0.51970 / 0.27 (46180) hydrogen bonds : bond 0.03201 / 2.13 ( 1172) hydrogen bonds : angle 5.35542 / 3.77 ( 3132) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 1.285 Fit side-chains REVERT: A 237 ARG cc_start: 0.7190 (mtp85) cc_final: 0.6989 (mtp-110) REVERT: A 251 ARG cc_start: 0.6215 (mmm-85) cc_final: 0.5890 (mmp-170) REVERT: A 277 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5926 (pp20) REVERT: A 280 ASP cc_start: 0.6644 (m-30) cc_final: 0.6386 (m-30) REVERT: A 339 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7261 (m110) REVERT: A 542 MET cc_start: 0.7517 (ttp) cc_final: 0.7152 (ptm) REVERT: A 546 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (tp) REVERT: A 635 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7501 (p) REVERT: A 655 MET cc_start: 0.7196 (ttm) cc_final: 0.6992 (tmm) REVERT: A 768 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6639 (tmm) REVERT: A 965 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 977 HIS cc_start: 0.7166 (p-80) cc_final: 0.6947 (p-80) REVERT: B 251 ARG cc_start: 0.6296 (mmm-85) cc_final: 0.5971 (mmp-170) REVERT: B 546 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 635 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 768 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6647 (tmm) REVERT: B 965 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 977 HIS cc_start: 0.7152 (p-80) cc_final: 0.6934 (p-80) REVERT: C 251 ARG cc_start: 0.6255 (mmm-85) cc_final: 0.5857 (mmp-170) REVERT: C 277 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5834 (pp20) REVERT: C 339 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7233 (m110) REVERT: C 542 MET cc_start: 0.7578 (ttp) cc_final: 0.7190 (ptm) REVERT: C 546 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8147 (tp) REVERT: C 635 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7513 (p) REVERT: C 655 MET cc_start: 0.7194 (ttm) cc_final: 0.6989 (tmm) REVERT: C 768 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6659 (tmm) REVERT: C 965 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 977 HIS cc_start: 0.7166 (p-80) cc_final: 0.6949 (p-80) REVERT: D 251 ARG cc_start: 0.6283 (mmm-85) cc_final: 0.5958 (mmp-170) REVERT: D 280 ASP cc_start: 0.6683 (m-30) cc_final: 0.6424 (m-30) REVERT: D 338 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7268 (mm-30) REVERT: D 542 MET cc_start: 0.7592 (ttp) cc_final: 0.7205 (ptm) REVERT: D 546 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8154 (tp) REVERT: D 635 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7519 (p) REVERT: D 655 MET cc_start: 0.7193 (ttm) cc_final: 0.6990 (tmm) REVERT: D 768 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: D 965 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 977 HIS cc_start: 0.7171 (p-80) cc_final: 0.6953 (p-80) REVERT: D 1013 ARG cc_start: 0.6739 (mtm-85) cc_final: 0.6327 (mtm-85) outliers start: 49 outliers final: 17 residues processed: 268 average time/residue: 0.8022 time to fit residues: 248.6001 Evaluate side-chains 256 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 394 ASN A 624 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN C 394 ASN C 624 GLN D 394 ASN D 624 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066519 restraints weight = 67293.148| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.91 r_work: 0.3023 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 33848 Z= 0.254 Angle : 0.643 7.211 46180 Z= 0.338 Chirality : 0.048 0.172 4840 Planarity : 0.005 0.051 6092 Dihedral : 5.472 20.994 4564 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 13.16 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4080 helix: -0.86 (0.20), residues: 516 sheet: -0.37 (0.14), residues: 1368 loop : -0.11 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1013 TYR 0.019 0.003 TYR C 856 PHE 0.018 0.002 PHE B 989 TRP 0.025 0.002 TRP B 553 HIS 0.006 0.002 HIS C 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (33844) covalent geometry : angle 0.64288 / 0.34 (46180) hydrogen bonds : bond 0.03881 / 2.61 ( 1172) hydrogen bonds : angle 5.78345 / 4.07 ( 3132) Misc. bond : bond 0.00068 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 1.069 Fit side-chains REVERT: A 144 ASP cc_start: 0.7429 (m-30) cc_final: 0.7147 (m-30) REVERT: A 277 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5991 (pp20) REVERT: A 280 ASP cc_start: 0.6706 (m-30) cc_final: 0.6409 (m-30) REVERT: A 546 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 635 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 655 MET cc_start: 0.7250 (ttm) cc_final: 0.6928 (tmm) REVERT: A 768 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6692 (tmm) REVERT: B 144 ASP cc_start: 0.7414 (m-30) cc_final: 0.7145 (m-30) REVERT: B 274 PHE cc_start: 0.7436 (m-80) cc_final: 0.6917 (m-80) REVERT: B 546 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 768 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: B 965 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 144 ASP cc_start: 0.7474 (m-30) cc_final: 0.7192 (m-30) REVERT: C 277 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5894 (pp20) REVERT: C 546 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8106 (tp) REVERT: C 635 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7553 (p) REVERT: C 655 MET cc_start: 0.7291 (ttm) cc_final: 0.6967 (tmm) REVERT: C 768 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: C 965 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 280 ASP cc_start: 0.6672 (m-30) cc_final: 0.6381 (m-30) REVERT: D 338 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7284 (mm-30) REVERT: D 546 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8103 (tp) REVERT: D 635 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7547 (p) REVERT: D 655 MET cc_start: 0.7300 (ttm) cc_final: 0.6976 (tmm) REVERT: D 768 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6662 (tmm) REVERT: D 965 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7453 (tm-30) outliers start: 56 outliers final: 26 residues processed: 266 average time/residue: 0.7781 time to fit residues: 240.9653 Evaluate side-chains 258 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 87 optimal weight: 0.9990 chunk 342 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 112 optimal weight: 0.0040 chunk 195 optimal weight: 2.9990 chunk 405 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 373 optimal weight: 0.0670 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 394 ASN A 624 GLN A 775 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 624 GLN C 394 ASN C 624 GLN C 675 GLN C 775 GLN D 216 HIS D 394 ASN D 624 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.080170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068634 restraints weight = 66618.477| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.91 r_work: 0.3085 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33848 Z= 0.103 Angle : 0.507 7.500 46180 Z= 0.267 Chirality : 0.044 0.156 4840 Planarity : 0.004 0.052 6092 Dihedral : 4.845 19.525 4564 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.20 % Allowed : 13.59 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4080 helix: -0.05 (0.22), residues: 520 sheet: -0.17 (0.14), residues: 1340 loop : 0.00 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1013 TYR 0.014 0.001 TYR C 100 PHE 0.012 0.001 PHE A 747 TRP 0.033 0.002 TRP C 553 HIS 0.004 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (33844) covalent geometry : angle 0.50712 / 0.27 (46180) hydrogen bonds : bond 0.03024 / 2.00 ( 1172) hydrogen bonds : angle 5.23800 / 3.69 ( 3132) Misc. bond : bond 0.00032 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 1.167 Fit side-chains REVERT: A 251 ARG cc_start: 0.6200 (mmm-85) cc_final: 0.5895 (mmp-170) REVERT: A 277 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5804 (pp20) REVERT: A 280 ASP cc_start: 0.6584 (m-30) cc_final: 0.6364 (m-30) REVERT: A 339 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7361 (m110) REVERT: A 542 MET cc_start: 0.7569 (ttp) cc_final: 0.7219 (ptm) REVERT: A 546 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (tp) REVERT: A 965 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 251 ARG cc_start: 0.6284 (mmm-85) cc_final: 0.5936 (mmp-170) REVERT: B 339 ASN cc_start: 0.7566 (t0) cc_final: 0.7311 (m110) REVERT: B 546 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 635 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7418 (p) REVERT: B 965 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7473 (tm-30) REVERT: C 251 ARG cc_start: 0.6213 (mmm-85) cc_final: 0.5826 (mmp-170) REVERT: C 339 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7199 (m110) REVERT: C 542 MET cc_start: 0.7508 (ttp) cc_final: 0.7220 (ptm) REVERT: C 546 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8142 (tp) REVERT: C 635 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7504 (p) REVERT: C 965 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 251 ARG cc_start: 0.6265 (mmm-85) cc_final: 0.5922 (mmp-170) REVERT: D 280 ASP cc_start: 0.6575 (m-30) cc_final: 0.6342 (m-30) REVERT: D 542 MET cc_start: 0.7511 (ttp) cc_final: 0.7223 (ptm) REVERT: D 546 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8150 (tp) REVERT: D 635 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7506 (p) REVERT: D 965 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 42 outliers final: 17 residues processed: 258 average time/residue: 0.7789 time to fit residues: 233.6515 Evaluate side-chains 244 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 148 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 207 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 394 ASN A 624 GLN A 646 HIS A 761 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 646 HIS C 394 ASN C 624 GLN C 646 HIS D 394 ASN D 624 GLN D 646 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067560 restraints weight = 67217.217| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.91 r_work: 0.3059 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33848 Z= 0.167 Angle : 0.559 6.966 46180 Z= 0.292 Chirality : 0.045 0.158 4840 Planarity : 0.005 0.053 6092 Dihedral : 5.023 20.123 4564 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.20 % Allowed : 13.90 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4080 helix: -0.23 (0.22), residues: 520 sheet: -0.25 (0.14), residues: 1368 loop : 0.00 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 781 TYR 0.016 0.002 TYR C 856 PHE 0.013 0.002 PHE C 989 TRP 0.024 0.002 TRP C 553 HIS 0.005 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33844) covalent geometry : angle 0.55901 / 0.29 (46180) hydrogen bonds : bond 0.03357 / 2.24 ( 1172) hydrogen bonds : angle 5.41498 / 3.81 ( 3132) Misc. bond : bond 0.00033 / 0.02 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.904 Fit side-chains REVERT: A 144 ASP cc_start: 0.7423 (m-30) cc_final: 0.7132 (m-30) REVERT: A 251 ARG cc_start: 0.6185 (mmm-85) cc_final: 0.5875 (mmp-170) REVERT: A 277 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5782 (pp20) REVERT: A 280 ASP cc_start: 0.6664 (m-30) cc_final: 0.6427 (m-30) REVERT: A 339 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7344 (m110) REVERT: A 542 MET cc_start: 0.7618 (ttp) cc_final: 0.7196 (ptm) REVERT: A 546 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 144 ASP cc_start: 0.7403 (m-30) cc_final: 0.7099 (m-30) REVERT: B 237 ARG cc_start: 0.7265 (mtp85) cc_final: 0.7029 (mtp-110) REVERT: B 251 ARG cc_start: 0.6236 (mmm-85) cc_final: 0.5913 (mmp-170) REVERT: B 339 ASN cc_start: 0.7529 (t0) cc_final: 0.7234 (m110) REVERT: B 546 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8105 (tp) REVERT: C 144 ASP cc_start: 0.7426 (m-30) cc_final: 0.7120 (m-30) REVERT: C 339 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7242 (m110) REVERT: C 542 MET cc_start: 0.7582 (ttp) cc_final: 0.7175 (ptm) REVERT: C 546 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8107 (tp) REVERT: C 635 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7538 (p) REVERT: D 280 ASP cc_start: 0.6616 (m-30) cc_final: 0.6385 (m-30) REVERT: D 338 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7276 (mm-30) REVERT: D 542 MET cc_start: 0.7600 (ttp) cc_final: 0.7194 (ptm) REVERT: D 546 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8138 (tp) REVERT: D 635 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7507 (p) outliers start: 42 outliers final: 20 residues processed: 255 average time/residue: 0.7776 time to fit residues: 229.9545 Evaluate side-chains 232 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 136 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 396 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 624 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN C 394 ASN C 624 GLN D 394 ASN D 624 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067543 restraints weight = 66902.221| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.91 r_work: 0.3057 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 33848 Z= 0.195 Angle : 0.658 65.863 46180 Z= 0.362 Chirality : 0.045 0.368 4840 Planarity : 0.006 0.261 6092 Dihedral : 5.035 29.380 4564 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.09 % Allowed : 14.02 % Favored : 84.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4080 helix: -0.24 (0.22), residues: 520 sheet: -0.25 (0.14), residues: 1368 loop : -0.00 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 781 TYR 0.015 0.002 TYR D 856 PHE 0.013 0.002 PHE C 989 TRP 0.025 0.002 TRP C 553 HIS 0.004 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (33844) covalent geometry : angle 0.65843 / 0.36 (46180) hydrogen bonds : bond 0.03348 / 2.24 ( 1172) hydrogen bonds : angle 5.41374 / 3.81 ( 3132) Misc. bond : bond 0.00017 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10045.64 seconds wall clock time: 171 minutes 57.45 seconds (10317.45 seconds total)