Starting phenix.real_space_refine on Sat Mar 7 05:05:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.map" model { file = "/net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zxj_11522/03_2026/6zxj_11522.cif" } resolution = 3.5 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 24017 2.51 5 N 6635 2.21 5 O 7554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 206 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38244 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3963 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "H" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5618 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 681} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "I" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4879 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 987 Unresolved non-hydrogen angles: 1238 Unresolved non-hydrogen dihedrals: 807 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 17, 'GLU:plan': 37, 'ASP:plan': 26, 'TYR:plan': 8, 'ASN:plan1': 18, 'ARG:plan': 9, 'HIS:plan': 8, 'PHE:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 558 Time building chain proxies: 8.80, per 1000 atoms: 0.23 Number of scatterers: 38244 At special positions: 0 Unit cell: (182.97, 179.76, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 7554 8.00 N 6635 7.00 C 24017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 73 sheets defined 32.1% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.528A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 213' Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.556A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.903A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.847A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.519A pdb=" N PHE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.618A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.546A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 634 through 637 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.674A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.923A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 477 through 487 Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.784A pdb=" N THR B 517 " --> pdb=" O PRO B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.655A pdb=" N LEU B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.478A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.512A pdb=" N LYS B 637 " --> pdb=" O ASP B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.778A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.558A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.992A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 477 through 487 Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.868A pdb=" N THR C 517 " --> pdb=" O PRO C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.666A pdb=" N LEU C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 581 removed outlier: 4.557A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.558A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.517A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.763A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.853A pdb=" N THR D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.575A pdb=" N LEU D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.447A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 Processing helix chain 'D' and resid 634 through 637 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.898A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.916A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.809A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.589A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.455A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 Processing helix chain 'E' and resid 634 through 637 removed outlier: 3.501A pdb=" N LYS E 637 " --> pdb=" O ASP E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 634 through 637' Processing helix chain 'E' and resid 704 through 706 No H-bonds generated for 'chain 'E' and resid 704 through 706' Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 213 removed outlier: 3.881A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.587A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.925A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 477 through 487 Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 512 through 517 removed outlier: 3.753A pdb=" N THR F 517 " --> pdb=" O PRO F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.513A pdb=" N PHE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.486A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 213 removed outlier: 3.892A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.940A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.833A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.649A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 570 removed outlier: 3.676A pdb=" N LEU G 569 " --> pdb=" O GLN G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 581 removed outlier: 4.629A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 Processing helix chain 'G' and resid 634 through 637 removed outlier: 3.529A pdb=" N LYS G 637 " --> pdb=" O ASP G 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 634 through 637' Processing helix chain 'G' and resid 704 through 706 No H-bonds generated for 'chain 'G' and resid 704 through 706' Processing helix chain 'G' and resid 732 through 734 No H-bonds generated for 'chain 'G' and resid 732 through 734' Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 69 through 77 removed outlier: 4.347A pdb=" N MET H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.599A pdb=" N LYS H 103 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.125A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 168 through 179 removed outlier: 3.897A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.539A pdb=" N LYS H 195 " --> pdb=" O THR H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 250 through 261 removed outlier: 3.690A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 256 " --> pdb=" O ILE H 252 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.536A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 286 through 298 removed outlier: 3.601A pdb=" N GLN H 297 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.620A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 321 removed outlier: 4.085A pdb=" N GLU H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 327 removed outlier: 5.562A pdb=" N ASP H 325 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 326 " --> pdb=" O GLN H 323 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 327 " --> pdb=" O ILE H 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 322 through 327' Processing helix chain 'H' and resid 331 through 342 Processing helix chain 'H' and resid 343 through 345 No H-bonds generated for 'chain 'H' and resid 343 through 345' Processing helix chain 'H' and resid 371 through 381 removed outlier: 4.017A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 Processing helix chain 'H' and resid 405 through 423 Processing helix chain 'H' and resid 442 through 446 Processing helix chain 'H' and resid 447 through 452 removed outlier: 3.612A pdb=" N ALA H 452 " --> pdb=" O ALA H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.516A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 575 removed outlier: 3.796A pdb=" N ILE H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 608 removed outlier: 3.532A pdb=" N ILE H 595 " --> pdb=" O TYR H 591 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 Processing helix chain 'H' and resid 635 through 639 Processing helix chain 'H' and resid 640 through 647 removed outlier: 3.586A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.760A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS H 690 " --> pdb=" O HIS H 686 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 691 " --> pdb=" O GLU H 687 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 3.980A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 Processing helix chain 'H' and resid 748 through 759 removed outlier: 3.533A pdb=" N ARG H 752 " --> pdb=" O ASP H 748 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 770 removed outlier: 3.630A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 3.947A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.751A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.836A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.138A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 158 removed outlier: 3.633A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.587A pdb=" N ASN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 193 through 197 removed outlier: 3.595A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.599A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU I 207 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.544A pdb=" N GLN I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.269A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 251 Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.547A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 303 through 312 removed outlier: 3.900A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.136A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.849A pdb=" N SER I 327 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 338 Processing helix chain 'I' and resid 372 through 383 removed outlier: 3.863A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 396 Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 447 through 452 removed outlier: 3.677A pdb=" N ALA I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 551 through 574 removed outlier: 3.507A pdb=" N ILE I 555 " --> pdb=" O PRO I 551 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU I 574 " --> pdb=" O TRP I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 610 removed outlier: 3.924A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU I 601 " --> pdb=" O GLU I 597 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 624 Processing helix chain 'I' and resid 635 through 640 removed outlier: 4.831A pdb=" N ALA I 640 " --> pdb=" O LEU I 636 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 646 Processing helix chain 'I' and resid 648 through 652 Processing helix chain 'I' and resid 679 through 699 removed outlier: 3.599A pdb=" N GLY I 683 " --> pdb=" O ASN I 679 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 721 removed outlier: 4.224A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 725 removed outlier: 3.717A pdb=" N LEU I 725 " --> pdb=" O GLY I 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 722 through 725' Processing helix chain 'I' and resid 728 through 731 Processing helix chain 'I' and resid 732 through 745 Processing helix chain 'I' and resid 748 through 759 removed outlier: 3.549A pdb=" N ARG I 752 " --> pdb=" O ASP I 748 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL I 755 " --> pdb=" O GLU I 751 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN I 756 " --> pdb=" O ARG I 752 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 772 removed outlier: 4.078A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS I 771 " --> pdb=" O ASN I 767 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE I 772 " --> pdb=" O ASP I 768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.139A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.139A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.135A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.647A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=AA8, first strand: chain 'A' and resid 626 through 629 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.630A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 695 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 696 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 728 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 698 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.593A pdb=" N PHE B 202 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 394 removed outlier: 5.094A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 389 through 394 removed outlier: 5.094A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 458 through 462 removed outlier: 4.241A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 501 through 506 Processing sheet with id=AB6, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB7, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=AB8, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.673A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 696 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 728 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL B 698 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 197 Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 360 removed outlier: 6.870A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 389 through 394 removed outlier: 5.121A pdb=" N THR C 390 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 385 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 392 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR C 381 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 458 through 462 removed outlier: 4.099A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.636A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC7, first strand: chain 'C' and resid 596 through 598 removed outlier: 6.556A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.646A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 192 through 197 removed outlier: 3.556A pdb=" N PHE D 202 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 389 through 394 removed outlier: 5.085A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 267 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR D 295 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 265 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARG D 297 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N HIS D 263 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 389 through 394 removed outlier: 5.085A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 267 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR D 295 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 265 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARG D 297 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N HIS D 263 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 364 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 419 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.131A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.725A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD7, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AD8, first strand: chain 'D' and resid 628 through 629 Processing sheet with id=AD9, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.505A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA D 700 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 725 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 192 through 197 Processing sheet with id=AE2, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.015A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.015A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 419 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.087A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.677A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE7, first strand: chain 'E' and resid 596 through 598 Processing sheet with id=AE8, first strand: chain 'E' and resid 626 through 629 removed outlier: 3.501A pdb=" N LEU E 627 " --> pdb=" O ILE E 676 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.614A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL E 696 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 728 " --> pdb=" O VAL E 696 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL E 698 " --> pdb=" O ILE E 726 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 192 through 197 Processing sheet with id=AF2, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.034A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.034A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.127A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.632A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF7, first strand: chain 'F' and resid 596 through 598 Processing sheet with id=AF8, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AF9, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.784A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL F 696 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG2, first strand: chain 'G' and resid 389 through 394 removed outlier: 5.054A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 389 through 394 removed outlier: 5.054A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.267A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.628A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG7, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AG8, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AG9, first strand: chain 'G' and resid 654 through 655 removed outlier: 3.572A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 695 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 81 through 82 Processing sheet with id=AH2, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.627A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.627A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 485 through 486 Processing sheet with id=AH5, first strand: chain 'H' and resid 630 through 632 Processing sheet with id=AH6, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.567A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 103 through 105 Processing sheet with id=AH8, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.935A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU I 499 " --> pdb=" O MET I 441 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS I 540 " --> pdb=" O LYS I 536 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS I 536 " --> pdb=" O LYS I 540 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR I 542 " --> pdb=" O ILE I 534 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE I 534 " --> pdb=" O TYR I 542 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 544 " --> pdb=" O VAL I 532 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL I 532 " --> pdb=" O ARG I 544 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP I 546 " --> pdb=" O LYS I 530 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY I 526 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 485 through 487 Processing sheet with id=AI1, first strand: chain 'I' and resid 583 through 586 1510 hydrogen bonds defined for protein. 4164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.41 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6726 1.28 - 1.41: 9230 1.41 - 1.55: 22820 1.55 - 1.68: 33 1.68 - 1.81: 76 Bond restraints: 38885 Sorted by residual: bond pdb=" CB THR C 517 " pdb=" CG2 THR C 517 " ideal model delta sigma weight residual 1.521 1.402 0.119 3.30e-02 9.18e+02 1.31e+01 bond pdb=" N VAL I 119 " pdb=" CA VAL I 119 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" CB ILE B 183 " pdb=" CG2 ILE B 183 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.14e+01 bond pdb=" N VAL I 44 " pdb=" CA VAL I 44 " ideal model delta sigma weight residual 1.465 1.511 -0.046 1.38e-02 5.25e+03 1.13e+01 bond pdb=" CG1 ILE D 726 " pdb=" CD1 ILE D 726 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.11e+01 ... (remaining 38880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 51697 3.69 - 7.38: 1123 7.38 - 11.07: 78 11.07 - 14.76: 19 14.76 - 18.46: 5 Bond angle restraints: 52922 Sorted by residual: angle pdb=" N VAL I 44 " pdb=" CA VAL I 44 " pdb=" C VAL I 44 " ideal model delta sigma weight residual 106.55 118.78 -12.23 1.45e+00 4.76e-01 7.11e+01 angle pdb=" C ASN D 198 " pdb=" N LYS D 199 " pdb=" CA LYS D 199 " ideal model delta sigma weight residual 122.49 111.60 10.89 1.55e+00 4.16e-01 4.94e+01 angle pdb=" N LYS E 197 " pdb=" CA LYS E 197 " pdb=" C LYS E 197 " ideal model delta sigma weight residual 109.24 99.24 10.00 1.63e+00 3.76e-01 3.76e+01 angle pdb=" C VAL I 44 " pdb=" N LYS I 45 " pdb=" CA LYS I 45 " ideal model delta sigma weight residual 121.24 112.82 8.42 1.44e+00 4.82e-01 3.42e+01 angle pdb=" N GLU D 614 " pdb=" CA GLU D 614 " pdb=" CB GLU D 614 " ideal model delta sigma weight residual 110.22 118.88 -8.66 1.54e+00 4.22e-01 3.16e+01 ... (remaining 52917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 21983 18.06 - 36.13: 1358 36.13 - 54.19: 210 54.19 - 72.25: 40 72.25 - 90.31: 10 Dihedral angle restraints: 23601 sinusoidal: 8597 harmonic: 15004 Sorted by residual: dihedral pdb=" CA GLN H 165 " pdb=" C GLN H 165 " pdb=" N PRO H 166 " pdb=" CA PRO H 166 " ideal model delta harmonic sigma weight residual 0.00 37.35 -37.35 0 5.00e+00 4.00e-02 5.58e+01 dihedral pdb=" C VAL I 44 " pdb=" N VAL I 44 " pdb=" CA VAL I 44 " pdb=" CB VAL I 44 " ideal model delta harmonic sigma weight residual -122.00 -135.58 13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N VAL I 44 " pdb=" C VAL I 44 " pdb=" CA VAL I 44 " pdb=" CB VAL I 44 " ideal model delta harmonic sigma weight residual 123.40 135.48 -12.08 0 2.50e+00 1.60e-01 2.33e+01 ... (remaining 23598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4835 0.083 - 0.165: 1157 0.165 - 0.248: 178 0.248 - 0.330: 18 0.330 - 0.413: 2 Chirality restraints: 6190 Sorted by residual: chirality pdb=" CA VAL I 44 " pdb=" N VAL I 44 " pdb=" C VAL I 44 " pdb=" CB VAL I 44 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA LYS B 199 " pdb=" N LYS B 199 " pdb=" C LYS B 199 " pdb=" CB LYS B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LYS C 199 " pdb=" N LYS C 199 " pdb=" C LYS C 199 " pdb=" CB LYS C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 6187 not shown) Planarity restraints: 6947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.110 5.00e-02 4.00e+02 1.63e-01 4.24e+01 pdb=" N PRO I 385 " 0.281 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 513 " -0.033 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR I 513 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR I 513 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR I 513 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 513 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR I 513 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 513 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR I 513 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 44 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C VAL I 44 " -0.074 2.00e-02 2.50e+03 pdb=" O VAL I 44 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS I 45 " 0.025 2.00e-02 2.50e+03 ... (remaining 6944 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 688 2.62 - 3.19: 38207 3.19 - 3.76: 55776 3.76 - 4.33: 76886 4.33 - 4.90: 123712 Nonbonded interactions: 295269 Sorted by model distance: nonbonded pdb=" OE1 GLU H 374 " pdb=" NZ LYS H 378 " model vdw 2.048 3.120 nonbonded pdb=" OD1 ASP A 599 " pdb=" N ARG A 600 " model vdw 2.090 3.120 nonbonded pdb=" O ASN F 209 " pdb=" NZ LYS F 213 " model vdw 2.107 3.120 nonbonded pdb=" OD1 ASP B 185 " pdb=" N SER B 186 " model vdw 2.118 3.120 nonbonded pdb=" OD2 ASP B 195 " pdb=" OH TYR H 236 " model vdw 2.120 3.040 ... (remaining 295264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 175 through 722 or (resid 723 and (name N or name CA or na \ me C or name O or name CB )) or resid 724 through 734)) selection = (chain 'B' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) selection = (chain 'C' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'D' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'E' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) selection = (chain 'F' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'G' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) } ncs_group { reference = (chain 'H' and (resid 52 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )) or resid 74 through 79 or (r \ esid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thr \ ough 86 or (resid 87 through 90 and (name N or name CA or name C or name O or na \ me CB )) or resid 91 through 94 or (resid 95 through 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 or (resid 105 th \ rough 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ through 122 or (resid 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 126 and (name N or name CA or name C or na \ me O or name CB )) or resid 127 through 163 or (resid 164 through 165 and (name \ N or name CA or name C or name O or name CB )) or resid 166 through 192 or (resi \ d 193 and (name N or name CA or name C or name O or name CB )) or resid 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 249 or (resid 250 through 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 272 or (resid 273 and (name N or name CA or \ name C or name O or name CB )) or resid 274 through 283 or (resid 284 through 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 or (resi \ d 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thro \ ugh 294 or (resid 295 through 297 and (name N or name CA or name C or name O or \ name CB )) or resid 298 or (resid 299 through 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 338 or (resid 343 through 384 an \ d (name N or name CA or name C or name O or name CB )) or resid 385 through 387 \ or (resid 388 through 389 and (name N or name CA or name C or name O or name CB \ )) or resid 390 or (resid 391 and (name N or name CA or name C or name O or name \ CB )) or resid 392 or (resid 393 and (name N or name CA or name C or name O or \ name CB )) or resid 394 through 397 or resid 401 through 403 or (resid 404 and ( \ name N or name CA or name C or name O or name CB )) or resid 405 through 425 or \ (resid 426 through 427 and (name N or name CA or name C or name O or name CB )) \ or resid 428 or (resid 429 and (name N or name CA or name C or name O or name CB \ )) or resid 433 or (resid 434 through 435 and (name N or name CA or name C or n \ ame O or name CB )) or resid 436 through 445 or (resid 446 through 450 and (name \ N or name CA or name C or name O or name CB )) or (resid 451 through 453 and (n \ ame N or name CA or name C or name O or name CB )) or resid 454 through 456 or ( \ resid 457 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 478 or (resid 479 through 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 through 482 or (resid 483 through 487 an \ d (name N or name CA or name C or name O or name CB )) or resid 488 or (resid 48 \ 9 through 490 and (name N or name CA or name C or name O or name CB )) or resid \ 491 through 507 or (resid 508 through 511 and (name N or name CA or name C or na \ me O or name CB )) or resid 512 through 519 or (resid 520 and (name N or name CA \ or name C or name O or name CB )) or resid 521 through 523 or (resid 524 throug \ h 525 and (name N or name CA or name C or name O or name CB )) or resid 526 or ( \ resid 527 through 528 and (name N or name CA or name C or name O or name CB )) o \ r resid 529 through 557 or (resid 558 and (name N or name CA or name C or name O \ or name CB )) or resid 559 through 564 or (resid 565 and (name N or name CA or \ name C or name O or name CB )) or resid 566 or (resid 567 through 569 and (name \ N or name CA or name C or name O or name CB )) or resid 570 or (resid 571 throug \ h 574 and (name N or name CA or name C or name O or name CB )) or resid 575 thro \ ugh 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) o \ r resid 579 through 601 or (resid 602 through 604 and (name N or name CA or name \ C or name O or name CB )) or resid 605 or (resid 606 through 614 and (name N or \ name CA or name C or name O or name CB )) or resid 615 or (resid 616 through 61 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 618 through \ 622 or (resid 623 through 624 and (name N or name CA or name C or name O or name \ CB )) or resid 625 through 630 or (resid 631 through 636 and (name N or name CA \ or name C or name O or name CB )) or resid 637 or (resid 638 through 656 and (n \ ame N or name CA or name C or name O or name CB )) or resid 657 or (resid 658 th \ rough 663 and (name N or name CA or name C or name O or name CB )) or resid 664 \ or (resid 665 through 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 or (resid 671 through 673 and (name N or name CA or name C or na \ me O or name CB )) or resid 674 or (resid 675 through 682 and (name N or name CA \ or name C or name O or name CB )) or resid 683 through 684 or (resid 685 throug \ h 688 and (name N or name CA or name C or name O or name CB )) or resid 689 or ( \ resid 690 through 696 and (name N or name CA or name C or name O or name CB )) o \ r resid 697 or (resid 698 through 710 and (name N or name CA or name C or name O \ or name CB )) or resid 711 through 714 or (resid 715 through 721 and (name N or \ name CA or name C or name O or name CB )) or resid 722 or (resid 723 through 72 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 729 or (resi \ d 730 through 746 and (name N or name CA or name C or name O or name CB )) or re \ sid 747 through 748 or (resid 749 through 759 and (name N or name CA or name C o \ r name O or name CB )) or resid 760 or (resid 761 through 763 and (name N or nam \ e CA or name C or name O or name CB )) or resid 764 through 765 or (resid 766 th \ rough 767 and (name N or name CA or name C or name O or name CB )) or resid 768 \ through 773)) selection = (chain 'I' and (resid 52 through 87 or (resid 88 through 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 277 or (resid 278 throu \ gh 279 and (name N or name CA or name C or name O or name CB )) or resid 280 thr \ ough 539 or (resid 540 and (name N or name CA or name C or name O or name CB )) \ or resid 541 through 551 or (resid 552 and (name N or name CA or name C or name \ O or name CB )) or resid 553 through 753 or (resid 754 through 759 and (name N o \ r name CA or name C or name O or name CB )) or resid 760 through 773)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.930 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.016 0.190 38885 Z= 0.664 Angle : 1.305 18.456 52922 Z= 0.723 Chirality : 0.072 0.413 6190 Planarity : 0.008 0.163 6947 Dihedral : 12.146 90.314 13853 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.33 % Favored : 91.08 % Rotamer: Outliers : 0.26 % Allowed : 0.85 % Favored : 98.89 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -3.10 (0.10), residues: 5043 helix: -2.17 (0.13), residues: 1152 sheet: -1.18 (0.14), residues: 1183 loop : -2.45 (0.10), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 178 TYR 0.061 0.004 TYR H 591 PHE 0.043 0.004 PHE D 202 TRP 0.071 0.005 TRP H 570 HIS 0.020 0.004 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.01570 (38885) covalent geometry : angle 1.30537 (52922) hydrogen bonds : bond 0.19807 ( 1346) hydrogen bonds : angle 8.41821 ( 4164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 847 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7563 (ptp-170) cc_final: 0.7180 (ptm160) REVERT: A 180 ASN cc_start: 0.8715 (t0) cc_final: 0.8514 (t0) REVERT: A 389 GLN cc_start: 0.7424 (mp10) cc_final: 0.6780 (mp10) REVERT: A 415 ASN cc_start: 0.8721 (m110) cc_final: 0.8442 (m110) REVERT: A 472 ASP cc_start: 0.8068 (t0) cc_final: 0.7755 (t0) REVERT: A 497 ASP cc_start: 0.7884 (p0) cc_final: 0.7500 (p0) REVERT: B 291 LYS cc_start: 0.8307 (mptt) cc_final: 0.8039 (mmtt) REVERT: B 335 ASP cc_start: 0.8265 (t0) cc_final: 0.7694 (t0) REVERT: B 353 ASN cc_start: 0.8028 (t0) cc_final: 0.7758 (t0) REVERT: B 560 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 570 ASN cc_start: 0.9038 (m-40) cc_final: 0.8787 (m-40) REVERT: B 594 LYS cc_start: 0.8228 (ttmt) cc_final: 0.8023 (ttpt) REVERT: B 614 GLU cc_start: 0.8723 (mp0) cc_final: 0.8255 (mp0) REVERT: B 638 ILE cc_start: 0.8683 (pt) cc_final: 0.8238 (pt) REVERT: B 703 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7923 (mmtm) REVERT: B 722 LYS cc_start: 0.8785 (tptm) cc_final: 0.8532 (tppt) REVERT: C 389 GLN cc_start: 0.7901 (mp10) cc_final: 0.7510 (mp10) REVERT: C 434 MET cc_start: 0.7457 (ppp) cc_final: 0.7107 (ppp) REVERT: C 441 GLU cc_start: 0.8746 (mp0) cc_final: 0.8396 (mp0) REVERT: C 446 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7538 (mmtm) REVERT: C 449 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7530 (ttm-80) REVERT: C 451 ASP cc_start: 0.7968 (m-30) cc_final: 0.7560 (m-30) REVERT: C 560 GLN cc_start: 0.8032 (tp40) cc_final: 0.7502 (tp40) REVERT: C 593 ASP cc_start: 0.8308 (t0) cc_final: 0.8055 (t0) REVERT: C 599 ASP cc_start: 0.8883 (t70) cc_final: 0.8642 (t70) REVERT: C 608 ASP cc_start: 0.8348 (m-30) cc_final: 0.7649 (t0) REVERT: C 613 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8526 (ptpp) REVERT: C 627 LEU cc_start: 0.8378 (mm) cc_final: 0.8172 (mm) REVERT: C 705 ASN cc_start: 0.9044 (m110) cc_final: 0.8594 (m-40) REVERT: D 250 GLU cc_start: 0.7767 (pm20) cc_final: 0.7368 (mp0) REVERT: D 346 TRP cc_start: 0.8615 (m-10) cc_final: 0.8390 (m-10) REVERT: D 359 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7831 (mtp180) REVERT: D 389 GLN cc_start: 0.7730 (mp10) cc_final: 0.7282 (mp10) REVERT: D 434 MET cc_start: 0.7889 (ppp) cc_final: 0.7580 (ppp) REVERT: D 442 LEU cc_start: 0.8438 (tt) cc_final: 0.8119 (tt) REVERT: D 446 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7597 (mmmt) REVERT: D 447 GLN cc_start: 0.8683 (pp30) cc_final: 0.8327 (pp30) REVERT: D 448 LEU cc_start: 0.8594 (mp) cc_final: 0.8229 (mt) REVERT: D 509 ASN cc_start: 0.8742 (t0) cc_final: 0.8230 (t0) REVERT: D 633 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8299 (tppt) REVERT: D 703 LYS cc_start: 0.8384 (mptt) cc_final: 0.8042 (mptt) REVERT: D 727 PHE cc_start: 0.8290 (t80) cc_final: 0.7219 (t80) REVERT: E 328 ASN cc_start: 0.8476 (m-40) cc_final: 0.8230 (m110) REVERT: E 444 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8470 (ptpp) REVERT: E 446 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8085 (ttmm) REVERT: E 447 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7488 (tp-100) REVERT: E 470 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7374 (ptm-80) REVERT: E 472 ASP cc_start: 0.8422 (t0) cc_final: 0.8142 (t0) REVERT: E 599 ASP cc_start: 0.8640 (t70) cc_final: 0.7910 (p0) REVERT: E 600 ARG cc_start: 0.7721 (tpt90) cc_final: 0.6683 (tpm170) REVERT: E 602 ASN cc_start: 0.8935 (m-40) cc_final: 0.8692 (m110) REVERT: E 613 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8653 (ptpp) REVERT: F 361 ASN cc_start: 0.8789 (t0) cc_final: 0.8537 (t0) REVERT: F 385 LEU cc_start: 0.8946 (tt) cc_final: 0.8653 (tt) REVERT: F 387 LYS cc_start: 0.9234 (mmpt) cc_final: 0.8752 (ptmm) REVERT: F 389 GLN cc_start: 0.7699 (mp10) cc_final: 0.7433 (mp10) REVERT: F 434 MET cc_start: 0.7880 (ppp) cc_final: 0.7666 (ppp) REVERT: F 438 GLN cc_start: 0.8889 (mt0) cc_final: 0.8495 (mp10) REVERT: F 444 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8666 (ptpt) REVERT: F 447 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7031 (mm110) REVERT: F 470 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7446 (ptp-110) REVERT: F 472 ASP cc_start: 0.8331 (t0) cc_final: 0.7879 (t0) REVERT: F 479 GLU cc_start: 0.7833 (mp0) cc_final: 0.7520 (mp0) REVERT: F 557 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7575 (mm-40) REVERT: F 560 GLN cc_start: 0.8734 (tp40) cc_final: 0.7614 (tm-30) REVERT: F 602 ASN cc_start: 0.8974 (m110) cc_final: 0.8774 (m-40) REVERT: G 265 ASP cc_start: 0.7716 (t0) cc_final: 0.7390 (t0) REVERT: G 387 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8660 (tppt) REVERT: G 472 ASP cc_start: 0.8310 (t70) cc_final: 0.7961 (t0) REVERT: G 486 GLU cc_start: 0.8079 (tp30) cc_final: 0.7530 (tp30) REVERT: G 496 LYS cc_start: 0.9024 (tptt) cc_final: 0.8798 (tppt) REVERT: G 563 LYS cc_start: 0.8604 (mppt) cc_final: 0.8276 (mmtm) REVERT: G 569 LEU cc_start: 0.9395 (mt) cc_final: 0.9096 (mp) REVERT: G 593 ASP cc_start: 0.8468 (t0) cc_final: 0.8174 (t0) REVERT: G 705 ASN cc_start: 0.8820 (m-40) cc_final: 0.8601 (m-40) REVERT: H 138 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.8893 (m) REVERT: H 158 ASP cc_start: 0.7836 (t70) cc_final: 0.7308 (t70) REVERT: H 187 ASP cc_start: 0.8648 (m-30) cc_final: 0.8098 (m-30) REVERT: H 215 GLU cc_start: 0.8092 (pt0) cc_final: 0.7890 (pt0) REVERT: H 226 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7879 (tm-30) REVERT: H 268 TYR cc_start: 0.8951 (t80) cc_final: 0.8710 (t80) REVERT: H 533 GLN cc_start: 0.7512 (pm20) cc_final: 0.6843 (pm20) REVERT: H 548 LYS cc_start: 0.7250 (tppt) cc_final: 0.6957 (tptp) REVERT: H 589 ASN cc_start: 0.8972 (m-40) cc_final: 0.8707 (m110) REVERT: H 604 ASN cc_start: 0.8561 (m-40) cc_final: 0.8248 (m-40) REVERT: H 620 ASN cc_start: 0.8734 (m110) cc_final: 0.8454 (m-40) REVERT: H 678 ARG cc_start: 0.6619 (mpt180) cc_final: 0.6368 (mpt180) REVERT: H 765 PHE cc_start: 0.8377 (t80) cc_final: 0.8139 (t80) REVERT: I 118 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7438 (p90) REVERT: I 162 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8511 (mmmt) REVERT: I 472 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8365 (ptpp) REVERT: I 533 GLN cc_start: 0.8449 (pt0) cc_final: 0.8227 (pt0) REVERT: I 537 GLN cc_start: 0.6630 (tm-30) cc_final: 0.6393 (tm-30) REVERT: I 542 TYR cc_start: 0.7976 (m-80) cc_final: 0.7624 (m-80) REVERT: I 544 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7397 (tpp80) REVERT: I 764 GLN cc_start: 0.8940 (mp10) cc_final: 0.8733 (mp10) outliers start: 10 outliers final: 3 residues processed: 850 average time/residue: 0.2522 time to fit residues: 341.7067 Evaluate side-chains 716 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 711 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain I residue 118 TYR Chi-restraints excluded: chain I residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 0.0050 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN D 541 GLN D 709 ASN E 415 ASN E 565 GLN E 570 ASN F 198 ASN F 326 ASN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 GLN F 560 GLN G 198 ASN H 132 GLN H 140 ASN H 228 GLN H 504 GLN H 567 ASN ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 GLN I 175 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN I 411 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.192856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111214 restraints weight = 58531.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116070 restraints weight = 28566.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119093 restraints weight = 19260.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120881 restraints weight = 15465.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121784 restraints weight = 13698.850| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38885 Z= 0.145 Angle : 0.723 10.485 52922 Z= 0.379 Chirality : 0.048 0.208 6190 Planarity : 0.005 0.086 6947 Dihedral : 4.904 38.402 5431 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 1.47 % Allowed : 9.71 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.44 (0.11), residues: 5043 helix: -0.42 (0.14), residues: 1243 sheet: -0.64 (0.14), residues: 1188 loop : -1.33 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 502 TYR 0.029 0.001 TYR H 591 PHE 0.032 0.002 PHE I 765 TRP 0.029 0.001 TRP H 570 HIS 0.007 0.001 HIS I 280 Details of bonding type rmsd covalent geometry : bond 0.00310 (38885) covalent geometry : angle 0.72268 (52922) hydrogen bonds : bond 0.04718 ( 1346) hydrogen bonds : angle 5.91566 ( 4164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 869 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7731 (ptp-170) cc_final: 0.7353 (ptm160) REVERT: A 180 ASN cc_start: 0.8675 (t0) cc_final: 0.8380 (t0) REVERT: A 224 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 389 GLN cc_start: 0.7401 (mp10) cc_final: 0.6816 (mp10) REVERT: A 415 ASN cc_start: 0.8819 (m110) cc_final: 0.8533 (m110) REVERT: A 434 MET cc_start: 0.7255 (ppp) cc_final: 0.6424 (ppp) REVERT: A 436 TYR cc_start: 0.8294 (t80) cc_final: 0.7939 (t80) REVERT: A 453 ASP cc_start: 0.8494 (p0) cc_final: 0.8170 (p0) REVERT: A 555 ASP cc_start: 0.7413 (t0) cc_final: 0.7082 (t0) REVERT: A 643 ILE cc_start: 0.8687 (mm) cc_final: 0.8331 (pt) REVERT: A 703 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8070 (mmtm) REVERT: B 224 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 335 ASP cc_start: 0.8202 (t0) cc_final: 0.7657 (t0) REVERT: B 353 ASN cc_start: 0.8370 (t0) cc_final: 0.8118 (t0) REVERT: B 434 MET cc_start: 0.8252 (ppp) cc_final: 0.8027 (ppp) REVERT: B 442 LEU cc_start: 0.8860 (tp) cc_final: 0.8508 (tt) REVERT: B 446 LYS cc_start: 0.8136 (mmpt) cc_final: 0.7657 (mmpt) REVERT: B 479 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 515 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 525 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7223 (mt-10) REVERT: B 546 ASP cc_start: 0.8270 (t70) cc_final: 0.8012 (t0) REVERT: B 594 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8116 (ttpt) REVERT: B 613 LYS cc_start: 0.9364 (mttt) cc_final: 0.9143 (ptpt) REVERT: B 614 GLU cc_start: 0.8582 (mp0) cc_final: 0.8321 (mp0) REVERT: B 703 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8019 (mmtm) REVERT: C 178 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7746 (mtt180) REVERT: C 326 ASN cc_start: 0.8824 (p0) cc_final: 0.8441 (p0) REVERT: C 385 LEU cc_start: 0.8659 (tt) cc_final: 0.7908 (tt) REVERT: C 387 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8410 (tptt) REVERT: C 389 GLN cc_start: 0.7948 (mp10) cc_final: 0.7305 (mp10) REVERT: C 444 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.8988 (ptpp) REVERT: C 446 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8106 (mmtt) REVERT: C 451 ASP cc_start: 0.8008 (m-30) cc_final: 0.7718 (m-30) REVERT: C 496 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8909 (tppt) REVERT: C 520 ASP cc_start: 0.8065 (p0) cc_final: 0.7859 (p0) REVERT: C 582 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8674 (mmmm) REVERT: C 587 MET cc_start: 0.8490 (mtt) cc_final: 0.8151 (mtt) REVERT: C 599 ASP cc_start: 0.8925 (t70) cc_final: 0.8644 (t70) REVERT: C 613 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8600 (ptpp) REVERT: C 703 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7867 (mmtp) REVERT: D 202 PHE cc_start: 0.8676 (p90) cc_final: 0.8472 (p90) REVERT: D 250 GLU cc_start: 0.7506 (pm20) cc_final: 0.7287 (mp0) REVERT: D 326 ASN cc_start: 0.8760 (p0) cc_final: 0.7894 (p0) REVERT: D 346 TRP cc_start: 0.8393 (m-10) cc_final: 0.8065 (m-10) REVERT: D 389 GLN cc_start: 0.7605 (mp10) cc_final: 0.7174 (mp10) REVERT: D 434 MET cc_start: 0.8063 (ppp) cc_final: 0.7740 (ppp) REVERT: D 446 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7994 (mmmt) REVERT: D 447 GLN cc_start: 0.8615 (pp30) cc_final: 0.8413 (pp30) REVERT: D 448 LEU cc_start: 0.8575 (mp) cc_final: 0.8133 (mp) REVERT: D 472 ASP cc_start: 0.7810 (t0) cc_final: 0.7227 (t0) REVERT: D 509 ASN cc_start: 0.8573 (t0) cc_final: 0.8273 (t0) REVERT: D 515 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7205 (mm-30) REVERT: D 555 ASP cc_start: 0.7136 (t0) cc_final: 0.6584 (t0) REVERT: D 592 ARG cc_start: 0.7625 (ptt180) cc_final: 0.7354 (ptt90) REVERT: D 633 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8315 (tptt) REVERT: D 643 ILE cc_start: 0.8967 (mm) cc_final: 0.8734 (pt) REVERT: D 703 LYS cc_start: 0.8521 (mptt) cc_final: 0.8167 (mptt) REVERT: D 727 PHE cc_start: 0.8490 (t80) cc_final: 0.7713 (t80) REVERT: E 213 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8623 (mmtm) REVERT: E 446 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8461 (ttmt) REVERT: E 447 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7551 (tp-100) REVERT: E 472 ASP cc_start: 0.8176 (t0) cc_final: 0.7590 (t0) REVERT: E 496 LYS cc_start: 0.8832 (tppt) cc_final: 0.8604 (tppt) REVERT: E 599 ASP cc_start: 0.8574 (t70) cc_final: 0.8148 (p0) REVERT: E 600 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7443 (tpm170) REVERT: E 602 ASN cc_start: 0.8890 (m-40) cc_final: 0.8427 (m-40) REVERT: E 633 LYS cc_start: 0.8961 (pptt) cc_final: 0.8284 (tptp) REVERT: E 638 ILE cc_start: 0.7610 (pt) cc_final: 0.7403 (pt) REVERT: E 643 ILE cc_start: 0.7740 (tp) cc_final: 0.7444 (pt) REVERT: F 195 ASP cc_start: 0.8061 (t0) cc_final: 0.7801 (t0) REVERT: F 387 LYS cc_start: 0.9268 (mmpt) cc_final: 0.8842 (ptmm) REVERT: F 434 MET cc_start: 0.7767 (ppp) cc_final: 0.7545 (ppp) REVERT: F 479 GLU cc_start: 0.8159 (mp0) cc_final: 0.7892 (mp0) REVERT: F 594 LYS cc_start: 0.8252 (ptpt) cc_final: 0.8009 (pmmt) REVERT: F 602 ASN cc_start: 0.8858 (m110) cc_final: 0.8647 (m-40) REVERT: G 265 ASP cc_start: 0.7707 (t0) cc_final: 0.7290 (t0) REVERT: G 291 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8298 (mmmt) REVERT: G 389 GLN cc_start: 0.8340 (mp10) cc_final: 0.7984 (mp10) REVERT: G 434 MET cc_start: 0.7009 (tmm) cc_final: 0.6631 (tmm) REVERT: G 472 ASP cc_start: 0.7673 (t70) cc_final: 0.7250 (t0) REVERT: G 486 GLU cc_start: 0.8052 (tp30) cc_final: 0.7609 (tp30) REVERT: G 496 LYS cc_start: 0.8987 (tptt) cc_final: 0.8641 (tppt) REVERT: G 555 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.5785 (t70) REVERT: G 556 GLN cc_start: 0.8037 (pm20) cc_final: 0.7468 (pm20) REVERT: G 557 GLN cc_start: 0.8137 (mp10) cc_final: 0.7825 (mp10) REVERT: G 560 GLN cc_start: 0.8797 (tp40) cc_final: 0.8488 (tp40) REVERT: G 563 LYS cc_start: 0.8665 (mppt) cc_final: 0.8453 (mmtp) REVERT: G 593 ASP cc_start: 0.8389 (t0) cc_final: 0.7981 (t0) REVERT: G 705 ASN cc_start: 0.8874 (m-40) cc_final: 0.8315 (p0) REVERT: H 118 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6118 (p90) REVERT: H 123 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8150 (mp0) REVERT: H 158 ASP cc_start: 0.7629 (t70) cc_final: 0.7149 (t70) REVERT: H 187 ASP cc_start: 0.8471 (m-30) cc_final: 0.7971 (m-30) REVERT: H 215 GLU cc_start: 0.7962 (pt0) cc_final: 0.7575 (pp20) REVERT: H 246 LYS cc_start: 0.8604 (tmmt) cc_final: 0.8316 (tmmt) REVERT: H 268 TYR cc_start: 0.8733 (t80) cc_final: 0.8479 (t80) REVERT: H 273 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8590 (ptpp) REVERT: H 488 ILE cc_start: 0.7499 (tt) cc_final: 0.6660 (tt) REVERT: H 548 LYS cc_start: 0.7606 (tppt) cc_final: 0.7295 (tptp) REVERT: H 604 ASN cc_start: 0.8749 (m-40) cc_final: 0.8494 (m-40) REVERT: H 772 PHE cc_start: 0.8403 (m-80) cc_final: 0.8006 (m-80) REVERT: I 61 LYS cc_start: 0.8951 (tppt) cc_final: 0.8526 (tppt) REVERT: I 65 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8718 (mmmt) REVERT: I 118 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7862 (p90) REVERT: I 162 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8404 (mmmt) REVERT: I 167 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6317 (t80) REVERT: I 182 ASP cc_start: 0.7582 (t0) cc_final: 0.7324 (t70) REVERT: I 194 LEU cc_start: 0.8916 (mt) cc_final: 0.8700 (mt) REVERT: I 261 ASP cc_start: 0.8513 (t70) cc_final: 0.8242 (t0) REVERT: I 475 PHE cc_start: 0.8080 (t80) cc_final: 0.7658 (t80) REVERT: I 531 ASP cc_start: 0.7787 (t70) cc_final: 0.7553 (t70) REVERT: I 533 GLN cc_start: 0.8537 (pt0) cc_final: 0.8134 (pt0) REVERT: I 537 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6486 (tm-30) REVERT: I 542 TYR cc_start: 0.8134 (m-80) cc_final: 0.7842 (m-80) outliers start: 57 outliers final: 32 residues processed: 894 average time/residue: 0.2378 time to fit residues: 342.4066 Evaluate side-chains 791 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 754 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 563 LYS Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 555 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 118 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 405 ASN Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 420 optimal weight: 0.0670 chunk 245 optimal weight: 0.7980 chunk 273 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 282 optimal weight: 0.4980 chunk 384 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 462 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN C 246 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN D 499 ASN D 561 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 HIS ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 GLN H 567 ASN ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.193650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112812 restraints weight = 58039.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117598 restraints weight = 28401.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120621 restraints weight = 19110.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122298 restraints weight = 15271.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123434 restraints weight = 13534.279| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38885 Z= 0.120 Angle : 0.634 8.725 52922 Z= 0.330 Chirality : 0.046 0.190 6190 Planarity : 0.004 0.064 6947 Dihedral : 4.567 36.133 5430 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 12.98 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.83 (0.12), residues: 5043 helix: 0.07 (0.15), residues: 1287 sheet: -0.35 (0.14), residues: 1200 loop : -0.90 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 200 TYR 0.019 0.001 TYR G 542 PHE 0.030 0.001 PHE E 202 TRP 0.023 0.001 TRP H 570 HIS 0.017 0.001 HIS I 424 Details of bonding type rmsd covalent geometry : bond 0.00266 (38885) covalent geometry : angle 0.63397 (52922) hydrogen bonds : bond 0.03761 ( 1346) hydrogen bonds : angle 5.29094 ( 4164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 843 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7711 (ptp-170) cc_final: 0.7149 (ptm160) REVERT: A 180 ASN cc_start: 0.8692 (t0) cc_final: 0.8424 (t0) REVERT: A 224 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 363 ASN cc_start: 0.8897 (m-40) cc_final: 0.8638 (m-40) REVERT: A 385 LEU cc_start: 0.7870 (tt) cc_final: 0.7482 (tt) REVERT: A 389 GLN cc_start: 0.7447 (mp10) cc_final: 0.6815 (mp10) REVERT: A 434 MET cc_start: 0.7446 (ppp) cc_final: 0.6538 (ppp) REVERT: A 436 TYR cc_start: 0.8282 (t80) cc_final: 0.8024 (t80) REVERT: A 446 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8483 (mmpt) REVERT: A 453 ASP cc_start: 0.8617 (p0) cc_final: 0.8253 (p0) REVERT: A 582 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8928 (mmmm) REVERT: A 599 ASP cc_start: 0.7823 (t0) cc_final: 0.7500 (t70) REVERT: A 643 ILE cc_start: 0.8693 (mm) cc_final: 0.8388 (pt) REVERT: A 703 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8188 (mmtp) REVERT: B 224 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 291 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8000 (tppt) REVERT: B 292 ASN cc_start: 0.8195 (m-40) cc_final: 0.7601 (p0) REVERT: B 335 ASP cc_start: 0.8206 (t0) cc_final: 0.7128 (t0) REVERT: B 353 ASN cc_start: 0.8334 (t0) cc_final: 0.8055 (t0) REVERT: B 434 MET cc_start: 0.8505 (ppp) cc_final: 0.8240 (ppp) REVERT: B 515 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 525 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7236 (mt-10) REVERT: B 546 ASP cc_start: 0.8305 (t70) cc_final: 0.7969 (t0) REVERT: B 594 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8186 (ttpt) REVERT: B 595 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8096 (ptt90) REVERT: B 613 LYS cc_start: 0.9345 (mttt) cc_final: 0.8943 (ptpt) REVERT: B 703 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8004 (mmtm) REVERT: B 723 LYS cc_start: 0.8995 (pttt) cc_final: 0.8781 (pttm) REVERT: C 291 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8652 (mtpt) REVERT: C 326 ASN cc_start: 0.8898 (p0) cc_final: 0.8613 (p0) REVERT: C 346 TRP cc_start: 0.8264 (m-10) cc_final: 0.7807 (m-10) REVERT: C 385 LEU cc_start: 0.8631 (tt) cc_final: 0.7887 (tt) REVERT: C 387 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8371 (tptt) REVERT: C 389 GLN cc_start: 0.7903 (mp10) cc_final: 0.7248 (mp10) REVERT: C 444 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9160 (ptpp) REVERT: C 446 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7996 (mmtt) REVERT: C 451 ASP cc_start: 0.7974 (m-30) cc_final: 0.7761 (m-30) REVERT: C 472 ASP cc_start: 0.7073 (t0) cc_final: 0.6788 (t70) REVERT: C 496 LYS cc_start: 0.9333 (ttmm) cc_final: 0.8995 (tppt) REVERT: C 520 ASP cc_start: 0.7999 (p0) cc_final: 0.7758 (p0) REVERT: C 546 ASP cc_start: 0.8265 (t0) cc_final: 0.8058 (t0) REVERT: C 582 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8645 (mmmm) REVERT: C 593 ASP cc_start: 0.8083 (t0) cc_final: 0.7743 (t0) REVERT: C 599 ASP cc_start: 0.8923 (t70) cc_final: 0.8651 (t70) REVERT: C 608 ASP cc_start: 0.7971 (m-30) cc_final: 0.7488 (t70) REVERT: C 613 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8648 (ptpp) REVERT: C 703 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7909 (mmtp) REVERT: D 202 PHE cc_start: 0.8671 (p90) cc_final: 0.8442 (p90) REVERT: D 212 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 250 GLU cc_start: 0.7543 (pm20) cc_final: 0.7239 (mp0) REVERT: D 359 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7922 (mtp180) REVERT: D 389 GLN cc_start: 0.7588 (mp10) cc_final: 0.7151 (mp10) REVERT: D 434 MET cc_start: 0.8078 (ppp) cc_final: 0.7559 (ppp) REVERT: D 444 LYS cc_start: 0.9020 (tppt) cc_final: 0.8799 (tppt) REVERT: D 446 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7948 (mmmt) REVERT: D 447 GLN cc_start: 0.8572 (pp30) cc_final: 0.8365 (pp30) REVERT: D 448 LEU cc_start: 0.8649 (mp) cc_final: 0.8181 (mp) REVERT: D 465 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7849 (mp0) REVERT: D 472 ASP cc_start: 0.7616 (t0) cc_final: 0.7256 (t0) REVERT: D 497 ASP cc_start: 0.7503 (p0) cc_final: 0.6982 (p0) REVERT: D 499 ASN cc_start: 0.8524 (m110) cc_final: 0.7537 (m-40) REVERT: D 515 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7340 (mm-30) REVERT: D 633 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8183 (tptt) REVERT: D 643 ILE cc_start: 0.8888 (mm) cc_final: 0.8642 (pt) REVERT: D 703 LYS cc_start: 0.8595 (mptt) cc_final: 0.8137 (mptt) REVERT: D 727 PHE cc_start: 0.8552 (t80) cc_final: 0.7870 (t80) REVERT: E 185 ASP cc_start: 0.8173 (p0) cc_final: 0.7949 (p0) REVERT: E 446 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8359 (mmtm) REVERT: E 447 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7604 (tp40) REVERT: E 454 GLN cc_start: 0.8852 (mp10) cc_final: 0.8551 (mp10) REVERT: E 479 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6718 (mt-10) REVERT: E 496 LYS cc_start: 0.8784 (tppt) cc_final: 0.8561 (tppt) REVERT: E 561 ASN cc_start: 0.7677 (t0) cc_final: 0.7386 (t0) REVERT: E 578 LEU cc_start: 0.8280 (tp) cc_final: 0.8071 (tt) REVERT: E 599 ASP cc_start: 0.8555 (t70) cc_final: 0.8162 (p0) REVERT: E 600 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7502 (tpm170) REVERT: E 602 ASN cc_start: 0.8946 (m-40) cc_final: 0.8310 (m110) REVERT: E 613 LYS cc_start: 0.8888 (pttm) cc_final: 0.8630 (pttm) REVERT: E 633 LYS cc_start: 0.8982 (pptt) cc_final: 0.8303 (tptp) REVERT: E 643 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7557 (pt) REVERT: F 178 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7348 (mtm180) REVERT: F 195 ASP cc_start: 0.8020 (t0) cc_final: 0.7714 (t0) REVERT: F 224 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7637 (mm-30) REVERT: F 326 ASN cc_start: 0.7484 (m-40) cc_final: 0.7226 (m110) REVERT: F 331 THR cc_start: 0.9090 (m) cc_final: 0.8802 (p) REVERT: F 361 ASN cc_start: 0.8723 (t0) cc_final: 0.8475 (m-40) REVERT: F 479 GLU cc_start: 0.8230 (mp0) cc_final: 0.7900 (mp0) REVERT: F 563 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (pptt) REVERT: F 579 ASP cc_start: 0.8370 (p0) cc_final: 0.8063 (t0) REVERT: F 593 ASP cc_start: 0.7799 (t0) cc_final: 0.7576 (t0) REVERT: F 599 ASP cc_start: 0.7986 (t0) cc_final: 0.7632 (t0) REVERT: G 387 LYS cc_start: 0.8774 (tppt) cc_final: 0.8550 (tppt) REVERT: G 389 GLN cc_start: 0.8334 (mp10) cc_final: 0.8045 (mp10) REVERT: G 446 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8348 (mmtt) REVERT: G 496 LYS cc_start: 0.9020 (tptt) cc_final: 0.8760 (tppt) REVERT: G 521 MET cc_start: 0.8220 (tpp) cc_final: 0.7515 (mpp) REVERT: G 556 GLN cc_start: 0.8031 (pm20) cc_final: 0.7764 (pm20) REVERT: G 593 ASP cc_start: 0.8240 (t0) cc_final: 0.7862 (t0) REVERT: G 703 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7807 (mttp) REVERT: G 705 ASN cc_start: 0.8873 (m-40) cc_final: 0.8651 (m110) REVERT: H 118 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6175 (p90) REVERT: H 158 ASP cc_start: 0.7630 (t70) cc_final: 0.7152 (t70) REVERT: H 187 ASP cc_start: 0.8413 (m-30) cc_final: 0.7940 (m-30) REVERT: H 215 GLU cc_start: 0.7903 (pt0) cc_final: 0.7606 (pp20) REVERT: H 246 LYS cc_start: 0.8602 (tmmt) cc_final: 0.8331 (tmmt) REVERT: H 268 TYR cc_start: 0.8848 (t80) cc_final: 0.8589 (t80) REVERT: H 273 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8523 (ptpp) REVERT: H 510 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.7184 (mmm160) REVERT: H 772 PHE cc_start: 0.8235 (m-80) cc_final: 0.7851 (m-80) REVERT: I 61 LYS cc_start: 0.8976 (tppt) cc_final: 0.8655 (tppt) REVERT: I 118 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7992 (p90) REVERT: I 162 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8468 (mmtp) REVERT: I 167 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.6014 (t80) REVERT: I 182 ASP cc_start: 0.7529 (t0) cc_final: 0.7263 (t70) REVERT: I 194 LEU cc_start: 0.8919 (mt) cc_final: 0.8692 (mt) REVERT: I 246 LYS cc_start: 0.8839 (tppt) cc_final: 0.8558 (tppt) REVERT: I 263 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8499 (mmm160) REVERT: I 472 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8095 (pttt) REVERT: I 475 PHE cc_start: 0.8082 (t80) cc_final: 0.7712 (t80) REVERT: I 531 ASP cc_start: 0.7806 (t70) cc_final: 0.7599 (t70) REVERT: I 533 GLN cc_start: 0.8618 (pt0) cc_final: 0.8256 (pt0) REVERT: I 537 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6466 (tm-30) REVERT: I 542 TYR cc_start: 0.8149 (m-80) cc_final: 0.7735 (m-80) REVERT: I 544 ARG cc_start: 0.7422 (tpp80) cc_final: 0.7169 (tpp80) outliers start: 96 outliers final: 56 residues processed: 894 average time/residue: 0.2425 time to fit residues: 350.5000 Evaluate side-chains 825 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 762 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 563 LYS Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 118 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 405 ASN Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 407 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 252 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 469 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN D 561 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS H 567 ASN H 588 HIS ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN I 424 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.192730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110057 restraints weight = 58932.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114877 restraints weight = 28841.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117830 restraints weight = 19567.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119620 restraints weight = 15774.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120604 restraints weight = 14064.484| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38885 Z= 0.128 Angle : 0.614 9.665 52922 Z= 0.319 Chirality : 0.046 0.270 6190 Planarity : 0.004 0.054 6947 Dihedral : 4.430 35.339 5428 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 2.74 % Allowed : 15.02 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.47 (0.12), residues: 5043 helix: 0.36 (0.15), residues: 1279 sheet: -0.07 (0.14), residues: 1207 loop : -0.71 (0.13), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 600 TYR 0.024 0.001 TYR D 542 PHE 0.032 0.001 PHE A 202 TRP 0.020 0.001 TRP H 570 HIS 0.008 0.001 HIS I 424 Details of bonding type rmsd covalent geometry : bond 0.00297 (38885) covalent geometry : angle 0.61404 (52922) hydrogen bonds : bond 0.03526 ( 1346) hydrogen bonds : angle 5.01972 ( 4164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 810 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7793 (ptp-170) cc_final: 0.7322 (ptm160) REVERT: A 180 ASN cc_start: 0.8711 (t0) cc_final: 0.8462 (t0) REVERT: A 224 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 363 ASN cc_start: 0.9021 (m-40) cc_final: 0.8489 (m-40) REVERT: A 389 GLN cc_start: 0.7444 (mp10) cc_final: 0.6861 (mp10) REVERT: A 434 MET cc_start: 0.7484 (ppp) cc_final: 0.6572 (ppp) REVERT: A 453 ASP cc_start: 0.8672 (p0) cc_final: 0.8297 (p0) REVERT: A 555 ASP cc_start: 0.7248 (t70) cc_final: 0.6904 (t70) REVERT: A 582 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8925 (mmmm) REVERT: A 599 ASP cc_start: 0.7834 (t0) cc_final: 0.7549 (t70) REVERT: A 636 ARG cc_start: 0.8597 (ptp90) cc_final: 0.8080 (ptp90) REVERT: A 637 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8982 (ttpt) REVERT: A 643 ILE cc_start: 0.8609 (mm) cc_final: 0.8388 (pt) REVERT: A 703 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8208 (mmtp) REVERT: A 709 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: B 224 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 291 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8076 (tppt) REVERT: B 292 ASN cc_start: 0.8046 (m-40) cc_final: 0.7494 (p0) REVERT: B 335 ASP cc_start: 0.8197 (t0) cc_final: 0.7308 (t0) REVERT: B 353 ASN cc_start: 0.8359 (t0) cc_final: 0.8079 (t0) REVERT: B 361 ASN cc_start: 0.8768 (t0) cc_final: 0.8059 (t0) REVERT: B 434 MET cc_start: 0.8541 (ppp) cc_final: 0.8301 (ppp) REVERT: B 446 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7878 (mmtt) REVERT: B 476 ASN cc_start: 0.7929 (t0) cc_final: 0.7668 (t0) REVERT: B 546 ASP cc_start: 0.8278 (t70) cc_final: 0.7893 (t0) REVERT: B 560 GLN cc_start: 0.7397 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 563 LYS cc_start: 0.8310 (pttm) cc_final: 0.8056 (pttt) REVERT: B 594 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8183 (ttpt) REVERT: B 595 ARG cc_start: 0.8562 (ptt-90) cc_final: 0.8132 (ptt90) REVERT: B 703 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7961 (mmtm) REVERT: C 326 ASN cc_start: 0.8935 (p0) cc_final: 0.8704 (p0) REVERT: C 385 LEU cc_start: 0.8586 (tt) cc_final: 0.7811 (tt) REVERT: C 389 GLN cc_start: 0.7953 (mp10) cc_final: 0.7275 (mp10) REVERT: C 446 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8032 (mmtt) REVERT: C 472 ASP cc_start: 0.6972 (t0) cc_final: 0.6666 (t70) REVERT: C 496 LYS cc_start: 0.9296 (ttmm) cc_final: 0.9024 (tppt) REVERT: C 546 ASP cc_start: 0.8229 (t0) cc_final: 0.7910 (t0) REVERT: C 582 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8757 (mptt) REVERT: C 593 ASP cc_start: 0.8088 (t0) cc_final: 0.7658 (t0) REVERT: C 705 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8833 (t0) REVERT: D 199 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7395 (mmtt) REVERT: D 202 PHE cc_start: 0.8757 (p90) cc_final: 0.8380 (p90) REVERT: D 326 ASN cc_start: 0.8610 (p0) cc_final: 0.8265 (p0) REVERT: D 335 ASP cc_start: 0.8105 (t0) cc_final: 0.7601 (t0) REVERT: D 434 MET cc_start: 0.8155 (ppp) cc_final: 0.7597 (ppp) REVERT: D 444 LYS cc_start: 0.9091 (tppt) cc_final: 0.8851 (tppt) REVERT: D 448 LEU cc_start: 0.8588 (mp) cc_final: 0.8131 (mp) REVERT: D 465 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7826 (mp0) REVERT: D 472 ASP cc_start: 0.7565 (t0) cc_final: 0.7131 (t0) REVERT: D 485 GLN cc_start: 0.8400 (mt0) cc_final: 0.7911 (mt0) REVERT: D 497 ASP cc_start: 0.7597 (p0) cc_final: 0.7074 (p0) REVERT: D 499 ASN cc_start: 0.8558 (m110) cc_final: 0.7422 (m-40) REVERT: D 515 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7405 (mm-30) REVERT: D 557 GLN cc_start: 0.7309 (mp10) cc_final: 0.7085 (mp10) REVERT: D 633 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8101 (tptt) REVERT: D 643 ILE cc_start: 0.8844 (mm) cc_final: 0.8595 (pt) REVERT: D 703 LYS cc_start: 0.8650 (mptt) cc_final: 0.8204 (mptt) REVERT: D 727 PHE cc_start: 0.8551 (t80) cc_final: 0.7835 (t80) REVERT: E 185 ASP cc_start: 0.8208 (p0) cc_final: 0.7971 (p0) REVERT: E 447 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7550 (tp40) REVERT: E 454 GLN cc_start: 0.8861 (mp10) cc_final: 0.8455 (mp10) REVERT: E 561 ASN cc_start: 0.7690 (t0) cc_final: 0.7413 (t0) REVERT: E 587 MET cc_start: 0.7861 (mtt) cc_final: 0.7661 (mtt) REVERT: E 602 ASN cc_start: 0.8940 (m-40) cc_final: 0.8460 (m-40) REVERT: E 613 LYS cc_start: 0.8924 (pttm) cc_final: 0.8664 (pttm) REVERT: E 643 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7423 (pt) REVERT: F 178 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7775 (mtm180) REVERT: F 195 ASP cc_start: 0.7985 (t0) cc_final: 0.7717 (t0) REVERT: F 224 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7648 (mm-30) REVERT: F 291 LYS cc_start: 0.8261 (mmmm) cc_final: 0.8050 (mmmm) REVERT: F 326 ASN cc_start: 0.7522 (m-40) cc_final: 0.7296 (m110) REVERT: F 331 THR cc_start: 0.9004 (m) cc_final: 0.8591 (p) REVERT: F 361 ASN cc_start: 0.8742 (t0) cc_final: 0.8443 (m-40) REVERT: F 387 LYS cc_start: 0.9294 (mmmt) cc_final: 0.8928 (ptmm) REVERT: F 434 MET cc_start: 0.7404 (ppp) cc_final: 0.6986 (ppp) REVERT: F 479 GLU cc_start: 0.8222 (mp0) cc_final: 0.7926 (mp0) REVERT: F 579 ASP cc_start: 0.8358 (p0) cc_final: 0.8053 (t0) REVERT: F 593 ASP cc_start: 0.7869 (t0) cc_final: 0.7597 (t0) REVERT: F 633 LYS cc_start: 0.8929 (tppt) cc_final: 0.8114 (tppt) REVERT: F 634 ASP cc_start: 0.9179 (p0) cc_final: 0.8815 (p0) REVERT: F 637 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8609 (mppt) REVERT: G 268 ASN cc_start: 0.8601 (p0) cc_final: 0.8111 (p0) REVERT: G 387 LYS cc_start: 0.8795 (tppt) cc_final: 0.8528 (tppt) REVERT: G 389 GLN cc_start: 0.8371 (mp10) cc_final: 0.8117 (mp10) REVERT: G 472 ASP cc_start: 0.7498 (t70) cc_final: 0.6872 (t70) REVERT: G 496 LYS cc_start: 0.9067 (tptt) cc_final: 0.8815 (tppt) REVERT: G 549 GLU cc_start: 0.8038 (mp0) cc_final: 0.7706 (tp30) REVERT: G 563 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8635 (mmtp) REVERT: G 582 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8495 (mmmm) REVERT: G 593 ASP cc_start: 0.8097 (t0) cc_final: 0.7548 (t0) REVERT: G 703 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: G 705 ASN cc_start: 0.8857 (m-40) cc_final: 0.8323 (p0) REVERT: H 187 ASP cc_start: 0.8493 (m-30) cc_final: 0.8015 (m-30) REVERT: H 215 GLU cc_start: 0.7879 (pt0) cc_final: 0.7615 (pp20) REVERT: H 246 LYS cc_start: 0.8625 (tmmt) cc_final: 0.8419 (tmmt) REVERT: H 268 TYR cc_start: 0.8877 (t80) cc_final: 0.8621 (t80) REVERT: H 273 LYS cc_start: 0.8878 (tttt) cc_final: 0.8541 (ptmt) REVERT: H 441 MET cc_start: 0.6687 (tmm) cc_final: 0.6379 (tpt) REVERT: H 510 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7189 (mmm-85) REVERT: H 548 LYS cc_start: 0.6745 (tptp) cc_final: 0.6524 (tptp) REVERT: H 581 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8158 (mmtm) REVERT: H 597 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7551 (tm-30) REVERT: H 632 THR cc_start: 0.8783 (p) cc_final: 0.8432 (t) REVERT: H 764 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: H 772 PHE cc_start: 0.8124 (m-80) cc_final: 0.7747 (m-80) REVERT: I 61 LYS cc_start: 0.8947 (tppt) cc_final: 0.8714 (tppt) REVERT: I 62 LEU cc_start: 0.8377 (tt) cc_final: 0.7740 (tp) REVERT: I 118 TYR cc_start: 0.8758 (p90) cc_final: 0.8214 (p90) REVERT: I 162 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8246 (mmmt) REVERT: I 167 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5891 (t80) REVERT: I 182 ASP cc_start: 0.7644 (t0) cc_final: 0.7317 (t70) REVERT: I 194 LEU cc_start: 0.8966 (mt) cc_final: 0.8739 (mt) REVERT: I 235 LEU cc_start: 0.8970 (tp) cc_final: 0.8761 (tp) REVERT: I 246 LYS cc_start: 0.8899 (tppt) cc_final: 0.8563 (tppt) REVERT: I 263 ARG cc_start: 0.8965 (mmm160) cc_final: 0.8462 (mmm160) REVERT: I 475 PHE cc_start: 0.8123 (t80) cc_final: 0.7837 (t80) REVERT: I 530 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7361 (mtmm) REVERT: I 533 GLN cc_start: 0.8637 (pt0) cc_final: 0.7948 (pt0) REVERT: I 537 GLN cc_start: 0.6965 (tm-30) cc_final: 0.6453 (tm-30) REVERT: I 542 TYR cc_start: 0.8187 (m-80) cc_final: 0.7783 (m-80) REVERT: I 544 ARG cc_start: 0.7398 (tpp80) cc_final: 0.7182 (tpp80) outliers start: 106 outliers final: 70 residues processed: 867 average time/residue: 0.2438 time to fit residues: 341.3305 Evaluate side-chains 844 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 768 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 705 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 219 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 308 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 496 optimal weight: 40.0000 chunk 424 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 399 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN C 438 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN F 602 ASN H 117 HIS H 567 ASN H 638 ASN H 745 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.190181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107792 restraints weight = 58593.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112367 restraints weight = 29078.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115208 restraints weight = 19894.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116859 restraints weight = 16156.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117804 restraints weight = 14412.492| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 38885 Z= 0.193 Angle : 0.629 10.993 52922 Z= 0.328 Chirality : 0.047 0.216 6190 Planarity : 0.004 0.049 6947 Dihedral : 4.450 36.099 5425 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.92 % Rotamer: Outliers : 3.33 % Allowed : 16.57 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.58 (0.12), residues: 5043 helix: 0.21 (0.15), residues: 1331 sheet: 0.12 (0.15), residues: 1163 loop : -0.90 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 200 TYR 0.025 0.001 TYR D 542 PHE 0.032 0.002 PHE I 247 TRP 0.019 0.001 TRP H 570 HIS 0.008 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00462 (38885) covalent geometry : angle 0.62852 (52922) hydrogen bonds : bond 0.03794 ( 1346) hydrogen bonds : angle 4.92325 ( 4164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 783 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7170 (ptm160) REVERT: A 180 ASN cc_start: 0.8734 (t0) cc_final: 0.8485 (t0) REVERT: A 224 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 363 ASN cc_start: 0.8989 (m-40) cc_final: 0.8755 (m-40) REVERT: A 389 GLN cc_start: 0.7528 (mp10) cc_final: 0.6974 (mp10) REVERT: A 453 ASP cc_start: 0.8743 (p0) cc_final: 0.8336 (p0) REVERT: A 555 ASP cc_start: 0.7363 (t70) cc_final: 0.7003 (t70) REVERT: A 599 ASP cc_start: 0.7881 (t0) cc_final: 0.7602 (t0) REVERT: A 636 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8078 (ptp90) REVERT: A 703 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8080 (mmtm) REVERT: B 212 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: B 224 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 291 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8151 (tppt) REVERT: B 292 ASN cc_start: 0.8167 (m-40) cc_final: 0.7625 (p0) REVERT: B 335 ASP cc_start: 0.8188 (t0) cc_final: 0.7311 (t0) REVERT: B 353 ASN cc_start: 0.8369 (t0) cc_final: 0.8068 (t0) REVERT: B 446 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7765 (mmtt) REVERT: B 546 ASP cc_start: 0.8349 (t70) cc_final: 0.7926 (t0) REVERT: B 551 ASP cc_start: 0.7538 (m-30) cc_final: 0.7116 (p0) REVERT: B 560 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 563 LYS cc_start: 0.8299 (pttm) cc_final: 0.8058 (pttt) REVERT: B 594 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8294 (ttpt) REVERT: B 595 ARG cc_start: 0.8607 (ptt-90) cc_final: 0.8190 (ptt90) REVERT: B 703 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8051 (mmtm) REVERT: B 723 LYS cc_start: 0.8919 (pttt) cc_final: 0.8678 (pttp) REVERT: C 291 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8663 (mtpt) REVERT: C 326 ASN cc_start: 0.8929 (p0) cc_final: 0.8681 (p0) REVERT: C 385 LEU cc_start: 0.8665 (tt) cc_final: 0.7950 (tt) REVERT: C 387 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8500 (tptt) REVERT: C 389 GLN cc_start: 0.7995 (mp10) cc_final: 0.7331 (mp10) REVERT: C 441 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8515 (mm-30) REVERT: C 444 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8835 (ptpp) REVERT: C 446 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8159 (mmtt) REVERT: C 472 ASP cc_start: 0.7150 (t0) cc_final: 0.6810 (t70) REVERT: C 496 LYS cc_start: 0.9315 (ttmm) cc_final: 0.9082 (tppt) REVERT: C 497 ASP cc_start: 0.8054 (p0) cc_final: 0.7296 (p0) REVERT: C 499 ASN cc_start: 0.8588 (m-40) cc_final: 0.8066 (m-40) REVERT: C 546 ASP cc_start: 0.8242 (t0) cc_final: 0.7923 (t0) REVERT: C 560 GLN cc_start: 0.7951 (tp40) cc_final: 0.7222 (tp40) REVERT: C 582 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8680 (mmmm) REVERT: C 593 ASP cc_start: 0.8123 (t0) cc_final: 0.7607 (t0) REVERT: C 608 ASP cc_start: 0.7991 (m-30) cc_final: 0.7538 (t70) REVERT: C 705 ASN cc_start: 0.9143 (m-40) cc_final: 0.8888 (t0) REVERT: D 326 ASN cc_start: 0.8609 (p0) cc_final: 0.8348 (p0) REVERT: D 389 GLN cc_start: 0.7744 (mp10) cc_final: 0.7304 (mp10) REVERT: D 434 MET cc_start: 0.8118 (ppp) cc_final: 0.7561 (ppp) REVERT: D 437 ASN cc_start: 0.8955 (m110) cc_final: 0.7869 (m-40) REVERT: D 446 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7462 (mmmt) REVERT: D 472 ASP cc_start: 0.7737 (t0) cc_final: 0.7337 (t0) REVERT: D 496 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8668 (tppt) REVERT: D 497 ASP cc_start: 0.7594 (p0) cc_final: 0.7038 (p0) REVERT: D 499 ASN cc_start: 0.8581 (m110) cc_final: 0.7436 (m-40) REVERT: D 515 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7486 (mm-30) REVERT: D 643 ILE cc_start: 0.8838 (mm) cc_final: 0.8589 (pt) REVERT: D 703 LYS cc_start: 0.8633 (mptt) cc_final: 0.8289 (mptt) REVERT: D 727 PHE cc_start: 0.8575 (t80) cc_final: 0.7864 (t80) REVERT: E 185 ASP cc_start: 0.8240 (p0) cc_final: 0.8032 (p0) REVERT: E 444 LYS cc_start: 0.8896 (pttm) cc_final: 0.8544 (ptpp) REVERT: E 446 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8215 (mmtt) REVERT: E 447 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7636 (tp40) REVERT: E 454 GLN cc_start: 0.8952 (mp10) cc_final: 0.8533 (mp10) REVERT: E 472 ASP cc_start: 0.7995 (t0) cc_final: 0.7497 (t0) REVERT: E 561 ASN cc_start: 0.7818 (t0) cc_final: 0.7511 (t0) REVERT: E 587 MET cc_start: 0.8009 (mtt) cc_final: 0.7793 (mtt) REVERT: E 599 ASP cc_start: 0.8609 (t0) cc_final: 0.8380 (t0) REVERT: E 600 ARG cc_start: 0.7508 (tpm170) cc_final: 0.6647 (tpm170) REVERT: E 602 ASN cc_start: 0.8953 (m-40) cc_final: 0.8352 (m-40) REVERT: E 643 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7361 (pt) REVERT: E 703 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8591 (mmtt) REVERT: F 291 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7900 (mmmm) REVERT: F 331 THR cc_start: 0.9134 (m) cc_final: 0.8707 (p) REVERT: F 387 LYS cc_start: 0.9347 (mmmt) cc_final: 0.8986 (ptmm) REVERT: F 434 MET cc_start: 0.7548 (ppp) cc_final: 0.7012 (ppp) REVERT: F 438 GLN cc_start: 0.8985 (mt0) cc_final: 0.8722 (mt0) REVERT: F 479 GLU cc_start: 0.8200 (mp0) cc_final: 0.7870 (mp0) REVERT: F 557 GLN cc_start: 0.6915 (mp10) cc_final: 0.6530 (mp10) REVERT: F 563 LYS cc_start: 0.8906 (pptt) cc_final: 0.8672 (pptt) REVERT: F 565 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8209 (mt0) REVERT: F 579 ASP cc_start: 0.8364 (p0) cc_final: 0.8039 (t0) REVERT: F 593 ASP cc_start: 0.7889 (t0) cc_final: 0.7629 (t0) REVERT: F 594 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7981 (ptpp) REVERT: F 596 PHE cc_start: 0.9086 (m-10) cc_final: 0.8820 (m-10) REVERT: F 633 LYS cc_start: 0.9007 (tppt) cc_final: 0.8770 (tppt) REVERT: G 224 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7677 (mm-30) REVERT: G 268 ASN cc_start: 0.8606 (p0) cc_final: 0.8204 (p0) REVERT: G 387 LYS cc_start: 0.8930 (tppt) cc_final: 0.8575 (tppt) REVERT: G 389 GLN cc_start: 0.8428 (mp10) cc_final: 0.8178 (mp10) REVERT: G 434 MET cc_start: 0.6861 (tmm) cc_final: 0.6245 (tmm) REVERT: G 472 ASP cc_start: 0.7741 (t70) cc_final: 0.7033 (t70) REVERT: G 496 LYS cc_start: 0.9133 (tptt) cc_final: 0.8823 (tppt) REVERT: G 582 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8557 (mmmm) REVERT: G 593 ASP cc_start: 0.8107 (t0) cc_final: 0.7706 (t0) REVERT: G 703 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: G 722 LYS cc_start: 0.8718 (tptp) cc_final: 0.8491 (tppt) REVERT: G 723 LYS cc_start: 0.8968 (mttt) cc_final: 0.8514 (mttp) REVERT: H 118 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6365 (p90) REVERT: H 187 ASP cc_start: 0.8532 (m-30) cc_final: 0.8042 (m-30) REVERT: H 215 GLU cc_start: 0.7906 (pt0) cc_final: 0.7643 (pp20) REVERT: H 246 LYS cc_start: 0.8589 (tmmt) cc_final: 0.8389 (tmmt) REVERT: H 268 TYR cc_start: 0.8866 (t80) cc_final: 0.8602 (t80) REVERT: H 273 LYS cc_start: 0.8875 (tttt) cc_final: 0.8524 (ptmt) REVERT: H 441 MET cc_start: 0.6730 (tmm) cc_final: 0.6038 (tmm) REVERT: H 472 LYS cc_start: 0.8697 (tttp) cc_final: 0.8496 (tppt) REVERT: H 510 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7007 (mmm-85) REVERT: H 597 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 632 THR cc_start: 0.8808 (p) cc_final: 0.8474 (t) REVERT: H 641 GLU cc_start: 0.8486 (mp0) cc_final: 0.7996 (pm20) REVERT: H 764 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: H 772 PHE cc_start: 0.8108 (m-80) cc_final: 0.7681 (m-80) REVERT: I 61 LYS cc_start: 0.9059 (tppt) cc_final: 0.8812 (tppt) REVERT: I 118 TYR cc_start: 0.8850 (p90) cc_final: 0.8348 (p90) REVERT: I 162 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8334 (mmmt) REVERT: I 167 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5761 (t80) REVERT: I 182 ASP cc_start: 0.7627 (t0) cc_final: 0.7356 (t70) REVERT: I 194 LEU cc_start: 0.8993 (mt) cc_final: 0.8749 (mt) REVERT: I 246 LYS cc_start: 0.8913 (tppt) cc_final: 0.8585 (tppt) REVERT: I 468 PHE cc_start: 0.8457 (t80) cc_final: 0.7732 (t80) REVERT: I 472 LYS cc_start: 0.8641 (ptpp) cc_final: 0.7867 (ptpp) REVERT: I 475 PHE cc_start: 0.8100 (t80) cc_final: 0.7856 (t80) REVERT: I 491 ARG cc_start: 0.7556 (ptp-170) cc_final: 0.7336 (ptp-170) REVERT: I 533 GLN cc_start: 0.8424 (pt0) cc_final: 0.8150 (pt0) REVERT: I 537 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6491 (tm-30) REVERT: I 542 TYR cc_start: 0.8155 (m-80) cc_final: 0.7506 (m-10) outliers start: 129 outliers final: 94 residues processed: 856 average time/residue: 0.2408 time to fit residues: 334.5906 Evaluate side-chains 835 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 735 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 415 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 345 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 431 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS H 248 ASN H 567 ASN I 424 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.192163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110110 restraints weight = 58733.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114835 restraints weight = 28734.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117787 restraints weight = 19490.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119499 restraints weight = 15707.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120413 restraints weight = 14004.199| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38885 Z= 0.128 Angle : 0.619 12.925 52922 Z= 0.316 Chirality : 0.046 0.333 6190 Planarity : 0.004 0.046 6947 Dihedral : 4.289 34.954 5424 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 3.15 % Allowed : 17.32 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 5043 helix: 0.44 (0.15), residues: 1289 sheet: 0.27 (0.15), residues: 1160 loop : -0.70 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 200 TYR 0.018 0.001 TYR D 542 PHE 0.025 0.001 PHE A 202 TRP 0.015 0.001 TRP H 570 HIS 0.015 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00297 (38885) covalent geometry : angle 0.61876 (52922) hydrogen bonds : bond 0.03291 ( 1346) hydrogen bonds : angle 4.80350 ( 4164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 795 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7107 (ptm160) REVERT: A 180 ASN cc_start: 0.8722 (t0) cc_final: 0.8471 (t0) REVERT: A 224 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 363 ASN cc_start: 0.9033 (m-40) cc_final: 0.8579 (m-40) REVERT: A 389 GLN cc_start: 0.7555 (mp10) cc_final: 0.7020 (mp10) REVERT: A 453 ASP cc_start: 0.8779 (p0) cc_final: 0.8405 (p0) REVERT: A 555 ASP cc_start: 0.7423 (t70) cc_final: 0.7046 (t70) REVERT: A 636 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8080 (ptp90) REVERT: A 637 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8959 (ttpt) REVERT: A 703 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8095 (mmtm) REVERT: B 224 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 292 ASN cc_start: 0.8098 (m-40) cc_final: 0.7755 (p0) REVERT: B 335 ASP cc_start: 0.8174 (t0) cc_final: 0.7533 (t0) REVERT: B 353 ASN cc_start: 0.8357 (t0) cc_final: 0.8062 (t0) REVERT: B 446 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7816 (mmtt) REVERT: B 546 ASP cc_start: 0.8311 (t70) cc_final: 0.7866 (t0) REVERT: B 551 ASP cc_start: 0.7578 (m-30) cc_final: 0.7125 (p0) REVERT: B 560 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6866 (tm-30) REVERT: B 563 LYS cc_start: 0.8313 (pttm) cc_final: 0.8013 (pttt) REVERT: B 594 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8287 (ttpt) REVERT: B 595 ARG cc_start: 0.8556 (ptt-90) cc_final: 0.8181 (ptt90) REVERT: B 703 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8089 (mmtm) REVERT: B 723 LYS cc_start: 0.8979 (pttt) cc_final: 0.8702 (pttp) REVERT: C 235 ASP cc_start: 0.7561 (m-30) cc_final: 0.6637 (m-30) REVERT: C 326 ASN cc_start: 0.8943 (p0) cc_final: 0.8708 (p0) REVERT: C 385 LEU cc_start: 0.8740 (tt) cc_final: 0.8038 (tt) REVERT: C 387 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8455 (tptt) REVERT: C 389 GLN cc_start: 0.8022 (mp10) cc_final: 0.7355 (mp10) REVERT: C 441 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8406 (mm-30) REVERT: C 444 LYS cc_start: 0.9098 (ptpp) cc_final: 0.8559 (ptpp) REVERT: C 446 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8112 (mmtt) REVERT: C 472 ASP cc_start: 0.7226 (t0) cc_final: 0.6873 (t70) REVERT: C 496 LYS cc_start: 0.9290 (ttmm) cc_final: 0.9085 (tppt) REVERT: C 546 ASP cc_start: 0.8218 (t0) cc_final: 0.7908 (t0) REVERT: C 560 GLN cc_start: 0.7911 (tp40) cc_final: 0.7181 (tp40) REVERT: C 582 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8662 (mmmm) REVERT: C 593 ASP cc_start: 0.8047 (t0) cc_final: 0.7562 (t0) REVERT: C 705 ASN cc_start: 0.9081 (m-40) cc_final: 0.8753 (p0) REVERT: D 250 GLU cc_start: 0.7577 (mp0) cc_final: 0.7346 (pm20) REVERT: D 359 ARG cc_start: 0.8462 (mtp180) cc_final: 0.8186 (mtp180) REVERT: D 389 GLN cc_start: 0.7757 (mp10) cc_final: 0.7170 (mp10) REVERT: D 434 MET cc_start: 0.8131 (ppp) cc_final: 0.7547 (ppp) REVERT: D 443 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8616 (mm-30) REVERT: D 446 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7647 (mmmt) REVERT: D 447 GLN cc_start: 0.8253 (pp30) cc_final: 0.7601 (tp-100) REVERT: D 472 ASP cc_start: 0.7617 (t0) cc_final: 0.7175 (t0) REVERT: D 496 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8661 (tppt) REVERT: D 497 ASP cc_start: 0.7564 (p0) cc_final: 0.6944 (p0) REVERT: D 499 ASN cc_start: 0.8562 (m110) cc_final: 0.7402 (m-40) REVERT: D 515 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7404 (mm-30) REVERT: D 633 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8017 (tppt) REVERT: D 643 ILE cc_start: 0.8717 (mm) cc_final: 0.8487 (pt) REVERT: D 703 LYS cc_start: 0.8653 (mptt) cc_final: 0.8351 (mptt) REVERT: D 722 LYS cc_start: 0.9038 (tptp) cc_final: 0.8664 (tptp) REVERT: D 727 PHE cc_start: 0.8597 (t80) cc_final: 0.7926 (t80) REVERT: E 434 MET cc_start: 0.7670 (tmm) cc_final: 0.7355 (tmm) REVERT: E 444 LYS cc_start: 0.8762 (pttm) cc_final: 0.8503 (ptpp) REVERT: E 446 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8168 (mmtt) REVERT: E 447 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7656 (tp40) REVERT: E 454 GLN cc_start: 0.8953 (mp10) cc_final: 0.8633 (mp10) REVERT: E 472 ASP cc_start: 0.8015 (t0) cc_final: 0.7474 (t0) REVERT: E 496 LYS cc_start: 0.8617 (tppt) cc_final: 0.8397 (tppt) REVERT: E 565 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: E 587 MET cc_start: 0.7967 (mtt) cc_final: 0.7767 (mtt) REVERT: E 599 ASP cc_start: 0.8547 (t0) cc_final: 0.8314 (t0) REVERT: E 600 ARG cc_start: 0.7440 (tpm170) cc_final: 0.6764 (tpm170) REVERT: E 602 ASN cc_start: 0.8968 (m-40) cc_final: 0.8384 (m110) REVERT: E 613 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8669 (pttm) REVERT: F 195 ASP cc_start: 0.8011 (t0) cc_final: 0.7761 (t0) REVERT: F 197 LYS cc_start: 0.8619 (tptp) cc_final: 0.8235 (tptp) REVERT: F 224 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 291 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7682 (mmmm) REVERT: F 331 THR cc_start: 0.9139 (m) cc_final: 0.8690 (p) REVERT: F 387 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8954 (ptmm) REVERT: F 389 GLN cc_start: 0.7734 (mp10) cc_final: 0.7477 (mp10) REVERT: F 438 GLN cc_start: 0.8982 (mt0) cc_final: 0.8645 (mt0) REVERT: F 449 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8371 (mtm-85) REVERT: F 479 GLU cc_start: 0.8215 (mp0) cc_final: 0.7785 (mp0) REVERT: F 557 GLN cc_start: 0.7043 (mp10) cc_final: 0.6708 (mp10) REVERT: F 563 LYS cc_start: 0.8882 (pptt) cc_final: 0.8595 (pptt) REVERT: F 565 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8239 (mt0) REVERT: F 579 ASP cc_start: 0.8327 (p0) cc_final: 0.8042 (t0) REVERT: F 593 ASP cc_start: 0.7945 (t0) cc_final: 0.7646 (t0) REVERT: F 594 LYS cc_start: 0.8259 (ptpt) cc_final: 0.7973 (ptpp) REVERT: F 596 PHE cc_start: 0.9074 (m-10) cc_final: 0.8839 (m-10) REVERT: F 633 LYS cc_start: 0.8948 (tppt) cc_final: 0.8744 (tppt) REVERT: G 224 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7613 (mm-30) REVERT: G 268 ASN cc_start: 0.8554 (p0) cc_final: 0.8219 (p0) REVERT: G 389 GLN cc_start: 0.8419 (mp10) cc_final: 0.8190 (mp10) REVERT: G 434 MET cc_start: 0.7005 (tmm) cc_final: 0.6452 (tmm) REVERT: G 470 ARG cc_start: 0.7042 (tpp-160) cc_final: 0.6627 (tpp-160) REVERT: G 472 ASP cc_start: 0.7377 (t70) cc_final: 0.6678 (t70) REVERT: G 496 LYS cc_start: 0.9103 (tptt) cc_final: 0.8779 (tppt) REVERT: G 582 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8590 (mmmm) REVERT: G 593 ASP cc_start: 0.7975 (t0) cc_final: 0.7555 (t0) REVERT: G 703 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7766 (mttp) REVERT: H 118 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6369 (p90) REVERT: H 248 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7315 (p0) REVERT: H 260 LYS cc_start: 0.9467 (mtmm) cc_final: 0.8958 (mtmt) REVERT: H 268 TYR cc_start: 0.8874 (t80) cc_final: 0.8591 (t80) REVERT: H 273 LYS cc_start: 0.8857 (tttt) cc_final: 0.8419 (ptmt) REVERT: H 441 MET cc_start: 0.6694 (tmm) cc_final: 0.6044 (tmm) REVERT: H 472 LYS cc_start: 0.8688 (tttp) cc_final: 0.8330 (mtpp) REVERT: H 548 LYS cc_start: 0.6408 (tptp) cc_final: 0.6037 (tptp) REVERT: H 597 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7533 (tm-30) REVERT: H 632 THR cc_start: 0.8715 (p) cc_final: 0.8423 (t) REVERT: H 641 GLU cc_start: 0.8520 (mp0) cc_final: 0.8013 (pm20) REVERT: H 742 ARG cc_start: 0.8996 (tmm-80) cc_final: 0.8388 (tmm-80) REVERT: H 764 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: H 772 PHE cc_start: 0.8109 (m-80) cc_final: 0.7715 (m-80) REVERT: I 61 LYS cc_start: 0.8983 (tppt) cc_final: 0.8717 (tppt) REVERT: I 162 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8196 (mmmt) REVERT: I 167 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5713 (t80) REVERT: I 182 ASP cc_start: 0.7676 (t0) cc_final: 0.7396 (t70) REVERT: I 194 LEU cc_start: 0.8976 (mt) cc_final: 0.8755 (mt) REVERT: I 246 LYS cc_start: 0.8930 (tppt) cc_final: 0.8612 (tppt) REVERT: I 475 PHE cc_start: 0.8111 (t80) cc_final: 0.7885 (t80) REVERT: I 533 GLN cc_start: 0.8359 (pt0) cc_final: 0.8073 (pt0) REVERT: I 537 GLN cc_start: 0.6923 (tm-30) cc_final: 0.5952 (tm-30) REVERT: I 542 TYR cc_start: 0.8199 (m-80) cc_final: 0.7110 (m-80) REVERT: I 764 GLN cc_start: 0.8951 (mp10) cc_final: 0.8622 (mp10) outliers start: 122 outliers final: 88 residues processed: 861 average time/residue: 0.2430 time to fit residues: 338.8035 Evaluate side-chains 840 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 746 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 192 optimal weight: 5.9990 chunk 498 optimal weight: 50.0000 chunk 366 optimal weight: 7.9990 chunk 409 optimal weight: 6.9990 chunk 237 optimal weight: 0.0030 chunk 299 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 500 optimal weight: 50.0000 chunk 200 optimal weight: 50.0000 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN H 117 HIS H 567 ASN I 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.189185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107458 restraints weight = 58804.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113281 restraints weight = 30463.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113444 restraints weight = 19359.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114901 restraints weight = 16749.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115446 restraints weight = 14856.086| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 38885 Z= 0.217 Angle : 0.660 14.212 52922 Z= 0.340 Chirality : 0.047 0.320 6190 Planarity : 0.004 0.092 6947 Dihedral : 4.416 36.432 5424 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 3.69 % Allowed : 18.07 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.45 (0.12), residues: 5043 helix: 0.28 (0.15), residues: 1331 sheet: 0.26 (0.15), residues: 1166 loop : -0.83 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 600 TYR 0.019 0.001 TYR D 542 PHE 0.034 0.002 PHE I 247 TRP 0.017 0.001 TRP H 570 HIS 0.008 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00522 (38885) covalent geometry : angle 0.65953 (52922) hydrogen bonds : bond 0.03703 ( 1346) hydrogen bonds : angle 4.85101 ( 4164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 751 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7222 (ptm160) REVERT: A 180 ASN cc_start: 0.8737 (t0) cc_final: 0.8490 (t0) REVERT: A 224 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8167 (mm-30) REVERT: A 363 ASN cc_start: 0.8993 (m-40) cc_final: 0.8787 (m-40) REVERT: A 389 GLN cc_start: 0.7629 (mp10) cc_final: 0.7030 (mp10) REVERT: A 446 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8400 (mmpt) REVERT: A 453 ASP cc_start: 0.8817 (p0) cc_final: 0.8384 (p0) REVERT: A 555 ASP cc_start: 0.7418 (t70) cc_final: 0.7011 (t70) REVERT: A 599 ASP cc_start: 0.7864 (t70) cc_final: 0.7602 (t70) REVERT: A 636 ARG cc_start: 0.8438 (ptp90) cc_final: 0.8043 (ptp90) REVERT: A 703 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8020 (mmtm) REVERT: B 224 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 291 LYS cc_start: 0.8044 (tppt) cc_final: 0.7135 (tppt) REVERT: B 292 ASN cc_start: 0.8249 (m-40) cc_final: 0.7888 (p0) REVERT: B 335 ASP cc_start: 0.8187 (t0) cc_final: 0.7507 (t0) REVERT: B 353 ASN cc_start: 0.8301 (t0) cc_final: 0.8063 (t0) REVERT: B 434 MET cc_start: 0.8503 (ppp) cc_final: 0.8224 (ppp) REVERT: B 446 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7588 (mmtt) REVERT: B 453 ASP cc_start: 0.8699 (p0) cc_final: 0.8361 (p0) REVERT: B 546 ASP cc_start: 0.8355 (t70) cc_final: 0.7890 (t0) REVERT: B 551 ASP cc_start: 0.7632 (m-30) cc_final: 0.7072 (p0) REVERT: B 560 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 563 LYS cc_start: 0.8322 (pttm) cc_final: 0.8006 (pmtt) REVERT: B 569 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8489 (mm) REVERT: B 594 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8229 (ttpt) REVERT: B 595 ARG cc_start: 0.8617 (ptt-90) cc_final: 0.8173 (ptt90) REVERT: B 703 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7871 (mmtm) REVERT: C 291 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8655 (mtpt) REVERT: C 326 ASN cc_start: 0.8970 (p0) cc_final: 0.8660 (p0) REVERT: C 387 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8433 (tptt) REVERT: C 441 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8493 (mm-30) REVERT: C 444 LYS cc_start: 0.9094 (ptpp) cc_final: 0.8567 (ptpp) REVERT: C 446 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8031 (mmtt) REVERT: C 472 ASP cc_start: 0.7318 (t0) cc_final: 0.6953 (t70) REVERT: C 496 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9087 (tppt) REVERT: C 497 ASP cc_start: 0.8149 (p0) cc_final: 0.7702 (p0) REVERT: C 499 ASN cc_start: 0.8580 (m-40) cc_final: 0.8222 (m-40) REVERT: C 546 ASP cc_start: 0.8275 (t0) cc_final: 0.7955 (t0) REVERT: C 560 GLN cc_start: 0.7957 (tp40) cc_final: 0.7219 (tp40) REVERT: C 582 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8676 (mmmm) REVERT: C 593 ASP cc_start: 0.8149 (t0) cc_final: 0.7538 (t0) REVERT: C 705 ASN cc_start: 0.9103 (m-40) cc_final: 0.8660 (p0) REVERT: C 722 LYS cc_start: 0.8335 (tppt) cc_final: 0.8078 (tppt) REVERT: D 267 GLU cc_start: 0.7904 (mp0) cc_final: 0.7604 (mp0) REVERT: D 389 GLN cc_start: 0.7673 (mp10) cc_final: 0.7219 (mp10) REVERT: D 434 MET cc_start: 0.8113 (ppp) cc_final: 0.7449 (ppp) REVERT: D 446 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7495 (mmmt) REVERT: D 472 ASP cc_start: 0.7710 (t0) cc_final: 0.7273 (t0) REVERT: D 496 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8829 (tppt) REVERT: D 497 ASP cc_start: 0.7540 (p0) cc_final: 0.7026 (p0) REVERT: D 499 ASN cc_start: 0.8578 (m110) cc_final: 0.7383 (m-40) REVERT: D 515 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 633 LYS cc_start: 0.8659 (ttpt) cc_final: 0.7961 (tppt) REVERT: D 643 ILE cc_start: 0.8587 (mm) cc_final: 0.8339 (pt) REVERT: D 703 LYS cc_start: 0.8540 (mptt) cc_final: 0.8306 (mptt) REVERT: D 727 PHE cc_start: 0.8577 (t80) cc_final: 0.7882 (t80) REVERT: E 185 ASP cc_start: 0.8192 (p0) cc_final: 0.7991 (p0) REVERT: E 434 MET cc_start: 0.7626 (tmm) cc_final: 0.7322 (tmm) REVERT: E 444 LYS cc_start: 0.8748 (pttm) cc_final: 0.8501 (ptpp) REVERT: E 446 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8053 (mmtt) REVERT: E 447 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7595 (tp40) REVERT: E 454 GLN cc_start: 0.9013 (mp10) cc_final: 0.8703 (mp10) REVERT: E 472 ASP cc_start: 0.8071 (t0) cc_final: 0.7547 (t0) REVERT: E 568 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 587 MET cc_start: 0.8132 (mtt) cc_final: 0.7891 (mtt) REVERT: E 600 ARG cc_start: 0.7499 (tpm170) cc_final: 0.6403 (tpm170) REVERT: E 602 ASN cc_start: 0.8956 (m-40) cc_final: 0.7998 (m110) REVERT: F 197 LYS cc_start: 0.8658 (tptp) cc_final: 0.8296 (tptp) REVERT: F 224 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7563 (mm-30) REVERT: F 291 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7720 (mmmm) REVERT: F 444 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8498 (ptpp) REVERT: F 449 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8293 (mtm-85) REVERT: F 479 GLU cc_start: 0.8215 (mp0) cc_final: 0.7879 (mp0) REVERT: F 512 ASP cc_start: 0.7487 (t0) cc_final: 0.7133 (t0) REVERT: F 551 ASP cc_start: 0.7743 (m-30) cc_final: 0.6985 (p0) REVERT: F 557 GLN cc_start: 0.7019 (mp10) cc_final: 0.6806 (mp10) REVERT: F 563 LYS cc_start: 0.8915 (pptt) cc_final: 0.8604 (pptt) REVERT: F 593 ASP cc_start: 0.7955 (t0) cc_final: 0.7655 (t0) REVERT: F 596 PHE cc_start: 0.9065 (m-10) cc_final: 0.8800 (m-10) REVERT: F 599 ASP cc_start: 0.8169 (t0) cc_final: 0.7963 (t0) REVERT: F 633 LYS cc_start: 0.8977 (tppt) cc_final: 0.8725 (tppt) REVERT: G 224 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7672 (mm-30) REVERT: G 268 ASN cc_start: 0.8541 (p0) cc_final: 0.8232 (p0) REVERT: G 389 GLN cc_start: 0.8484 (mp10) cc_final: 0.8206 (mp10) REVERT: G 434 MET cc_start: 0.7233 (tmm) cc_final: 0.6658 (tmm) REVERT: G 472 ASP cc_start: 0.7426 (t70) cc_final: 0.7012 (t70) REVERT: G 496 LYS cc_start: 0.9195 (tptt) cc_final: 0.8912 (tppt) REVERT: G 521 MET cc_start: 0.8189 (tpp) cc_final: 0.7458 (mpp) REVERT: G 582 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8649 (mmmm) REVERT: G 593 ASP cc_start: 0.8128 (t0) cc_final: 0.7743 (t0) REVERT: G 703 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7773 (mttp) REVERT: G 723 LYS cc_start: 0.8851 (mppt) cc_final: 0.8520 (mmtm) REVERT: H 118 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6317 (p90) REVERT: H 248 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.7919 (p0) REVERT: H 260 LYS cc_start: 0.9431 (mtmm) cc_final: 0.8976 (mtmt) REVERT: H 268 TYR cc_start: 0.9024 (t80) cc_final: 0.8690 (t80) REVERT: H 273 LYS cc_start: 0.8996 (tttt) cc_final: 0.8576 (ptmt) REVERT: H 441 MET cc_start: 0.6712 (tmm) cc_final: 0.5510 (tmm) REVERT: H 597 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7602 (tm-30) REVERT: H 632 THR cc_start: 0.8687 (p) cc_final: 0.8404 (t) REVERT: H 742 ARG cc_start: 0.9022 (tmm-80) cc_final: 0.8458 (tmm-80) REVERT: H 764 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: H 772 PHE cc_start: 0.8226 (m-80) cc_final: 0.7464 (m-80) REVERT: I 61 LYS cc_start: 0.8991 (tppt) cc_final: 0.8653 (tppt) REVERT: I 65 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8628 (mmmt) REVERT: I 102 LYS cc_start: 0.6861 (mttt) cc_final: 0.6557 (mttm) REVERT: I 162 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8200 (mmmt) REVERT: I 167 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.5901 (t80) REVERT: I 182 ASP cc_start: 0.7744 (t0) cc_final: 0.7437 (t70) REVERT: I 194 LEU cc_start: 0.9001 (mt) cc_final: 0.8778 (mt) REVERT: I 246 LYS cc_start: 0.8930 (tppt) cc_final: 0.8607 (tppt) REVERT: I 472 LYS cc_start: 0.8755 (ptpp) cc_final: 0.8487 (ptpp) REVERT: I 503 ILE cc_start: 0.8985 (tp) cc_final: 0.8783 (tp) REVERT: I 537 GLN cc_start: 0.6876 (tm-30) cc_final: 0.5918 (tm-30) REVERT: I 542 TYR cc_start: 0.8025 (m-80) cc_final: 0.6878 (m-80) REVERT: I 764 GLN cc_start: 0.8852 (mp10) cc_final: 0.8589 (mp10) outliers start: 143 outliers final: 113 residues processed: 836 average time/residue: 0.2386 time to fit residues: 324.9775 Evaluate side-chains 854 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 735 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 153 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 314 optimal weight: 2.9990 chunk 210 optimal weight: 0.3980 chunk 303 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 GLN F 602 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS H 228 GLN H 248 ASN H 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.191836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109820 restraints weight = 58273.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114533 restraints weight = 28503.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117399 restraints weight = 19336.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119102 restraints weight = 15664.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119925 restraints weight = 13965.752| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38885 Z= 0.122 Angle : 0.646 14.535 52922 Z= 0.327 Chirality : 0.046 0.371 6190 Planarity : 0.004 0.081 6947 Dihedral : 4.264 35.779 5424 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.97 % Allowed : 19.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.15 (0.12), residues: 5043 helix: 0.68 (0.16), residues: 1249 sheet: 0.42 (0.15), residues: 1155 loop : -0.68 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 200 TYR 0.018 0.001 TYR I 513 PHE 0.033 0.001 PHE I 247 TRP 0.014 0.001 TRP H 570 HIS 0.007 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00282 (38885) covalent geometry : angle 0.64596 (52922) hydrogen bonds : bond 0.03242 ( 1346) hydrogen bonds : angle 4.75355 ( 4164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 767 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7786 (ptp-170) cc_final: 0.7187 (ptm160) REVERT: A 180 ASN cc_start: 0.8727 (t0) cc_final: 0.8483 (t0) REVERT: A 224 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 389 GLN cc_start: 0.7645 (mp10) cc_final: 0.7097 (mp10) REVERT: A 453 ASP cc_start: 0.8794 (p0) cc_final: 0.8394 (p0) REVERT: A 555 ASP cc_start: 0.7290 (t70) cc_final: 0.6929 (t0) REVERT: A 586 LYS cc_start: 0.8608 (mttm) cc_final: 0.8406 (mmtp) REVERT: A 587 MET cc_start: 0.7853 (ptp) cc_final: 0.7553 (ptp) REVERT: A 599 ASP cc_start: 0.7875 (t70) cc_final: 0.7647 (t70) REVERT: A 636 ARG cc_start: 0.8493 (ptp90) cc_final: 0.8137 (ptp90) REVERT: A 703 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8135 (mmtm) REVERT: A 723 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7923 (mptt) REVERT: B 224 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 267 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7403 (tp30) REVERT: B 335 ASP cc_start: 0.8187 (t0) cc_final: 0.7860 (t0) REVERT: B 353 ASN cc_start: 0.8427 (t0) cc_final: 0.8223 (t0) REVERT: B 434 MET cc_start: 0.8485 (ppp) cc_final: 0.8258 (ppp) REVERT: B 446 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7707 (mmtt) REVERT: B 453 ASP cc_start: 0.8664 (p0) cc_final: 0.8301 (p0) REVERT: B 546 ASP cc_start: 0.8338 (t70) cc_final: 0.7885 (t0) REVERT: B 551 ASP cc_start: 0.7577 (m-30) cc_final: 0.7104 (p0) REVERT: B 563 LYS cc_start: 0.8286 (pttm) cc_final: 0.8064 (pttt) REVERT: B 594 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8261 (ttpt) REVERT: B 595 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8163 (ptt90) REVERT: B 703 LYS cc_start: 0.8433 (mmtm) cc_final: 0.7979 (mmtm) REVERT: C 291 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8706 (mtpt) REVERT: C 326 ASN cc_start: 0.8951 (p0) cc_final: 0.8684 (p0) REVERT: C 387 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8368 (tptt) REVERT: C 441 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8380 (mm-30) REVERT: C 444 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8565 (ptpp) REVERT: C 446 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8128 (mmtt) REVERT: C 472 ASP cc_start: 0.7268 (t0) cc_final: 0.6800 (t70) REVERT: C 496 LYS cc_start: 0.9280 (ttmm) cc_final: 0.9054 (tppt) REVERT: C 497 ASP cc_start: 0.8145 (p0) cc_final: 0.7871 (p0) REVERT: C 499 ASN cc_start: 0.8560 (m-40) cc_final: 0.8180 (m-40) REVERT: C 546 ASP cc_start: 0.8242 (t0) cc_final: 0.7952 (t0) REVERT: C 582 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8721 (mmmm) REVERT: C 593 ASP cc_start: 0.8086 (t0) cc_final: 0.7533 (t0) REVERT: C 705 ASN cc_start: 0.9089 (m-40) cc_final: 0.8749 (p0) REVERT: C 722 LYS cc_start: 0.8367 (tppt) cc_final: 0.8138 (tppt) REVERT: D 265 ASP cc_start: 0.7744 (t0) cc_final: 0.6849 (t0) REVERT: D 267 GLU cc_start: 0.7962 (mp0) cc_final: 0.7455 (mp0) REVERT: D 359 ARG cc_start: 0.8502 (mtp180) cc_final: 0.7833 (mtp180) REVERT: D 389 GLN cc_start: 0.7693 (mp10) cc_final: 0.7245 (mp10) REVERT: D 434 MET cc_start: 0.8131 (ppp) cc_final: 0.7520 (ppp) REVERT: D 446 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7599 (mmmt) REVERT: D 472 ASP cc_start: 0.7615 (t0) cc_final: 0.7195 (t0) REVERT: D 497 ASP cc_start: 0.7524 (p0) cc_final: 0.6965 (p0) REVERT: D 499 ASN cc_start: 0.8589 (m110) cc_final: 0.7353 (m-40) REVERT: D 515 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7416 (mm-30) REVERT: D 643 ILE cc_start: 0.8657 (mm) cc_final: 0.8452 (pt) REVERT: D 703 LYS cc_start: 0.8630 (mptt) cc_final: 0.8421 (mptt) REVERT: D 722 LYS cc_start: 0.9045 (tptp) cc_final: 0.8677 (tptp) REVERT: D 727 PHE cc_start: 0.8569 (t80) cc_final: 0.7965 (t80) REVERT: E 434 MET cc_start: 0.7810 (tmm) cc_final: 0.7517 (tmm) REVERT: E 444 LYS cc_start: 0.8724 (pttm) cc_final: 0.8456 (ptpp) REVERT: E 446 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8065 (mmtt) REVERT: E 447 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7648 (tp40) REVERT: E 454 GLN cc_start: 0.8971 (mp10) cc_final: 0.8649 (mp10) REVERT: E 472 ASP cc_start: 0.7998 (t0) cc_final: 0.7445 (t0) REVERT: E 565 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: E 599 ASP cc_start: 0.8461 (t0) cc_final: 0.8189 (t0) REVERT: E 600 ARG cc_start: 0.7517 (tpm170) cc_final: 0.6786 (tpm170) REVERT: E 602 ASN cc_start: 0.8933 (m-40) cc_final: 0.8057 (m110) REVERT: F 197 LYS cc_start: 0.8637 (tptp) cc_final: 0.8266 (tptp) REVERT: F 224 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7514 (mm-30) REVERT: F 291 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7668 (mmmm) REVERT: F 387 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9006 (ptmm) REVERT: F 388 ASN cc_start: 0.9088 (p0) cc_final: 0.8764 (p0) REVERT: F 449 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8321 (mtm-85) REVERT: F 479 GLU cc_start: 0.8219 (mp0) cc_final: 0.7924 (mp0) REVERT: F 563 LYS cc_start: 0.8906 (pptt) cc_final: 0.8585 (pptt) REVERT: F 593 ASP cc_start: 0.7860 (t0) cc_final: 0.7589 (t0) REVERT: F 633 LYS cc_start: 0.8991 (tppt) cc_final: 0.8718 (tppt) REVERT: G 224 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7610 (mm-30) REVERT: G 268 ASN cc_start: 0.8537 (p0) cc_final: 0.8192 (p0) REVERT: G 389 GLN cc_start: 0.8504 (mp10) cc_final: 0.8287 (mp10) REVERT: G 434 MET cc_start: 0.7102 (tmm) cc_final: 0.6519 (tmm) REVERT: G 470 ARG cc_start: 0.6836 (tpp-160) cc_final: 0.6610 (tpp-160) REVERT: G 472 ASP cc_start: 0.7286 (t70) cc_final: 0.6478 (t0) REVERT: G 496 LYS cc_start: 0.9146 (tptt) cc_final: 0.8770 (tppt) REVERT: G 521 MET cc_start: 0.8143 (tpp) cc_final: 0.7592 (mpp) REVERT: G 582 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8611 (mmmm) REVERT: G 584 ASN cc_start: 0.8361 (m-40) cc_final: 0.8061 (m-40) REVERT: G 593 ASP cc_start: 0.7975 (t0) cc_final: 0.7551 (t0) REVERT: G 600 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7517 (ttp80) REVERT: G 703 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7841 (mttp) REVERT: G 705 ASN cc_start: 0.8910 (m-40) cc_final: 0.8378 (p0) REVERT: G 722 LYS cc_start: 0.8574 (tptp) cc_final: 0.8045 (tppt) REVERT: H 61 LYS cc_start: 0.8885 (mptt) cc_final: 0.8663 (mmtm) REVERT: H 94 LEU cc_start: 0.8602 (tp) cc_final: 0.8283 (tp) REVERT: H 118 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6591 (p90) REVERT: H 122 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7144 (mtmt) REVERT: H 123 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: H 248 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7649 (p0) REVERT: H 251 GLU cc_start: 0.7675 (pp20) cc_final: 0.7367 (tm-30) REVERT: H 260 LYS cc_start: 0.9448 (mtmm) cc_final: 0.8967 (mtmt) REVERT: H 268 TYR cc_start: 0.8900 (t80) cc_final: 0.8608 (t80) REVERT: H 273 LYS cc_start: 0.9002 (tttt) cc_final: 0.8540 (ptmt) REVERT: H 472 LYS cc_start: 0.8653 (tttp) cc_final: 0.8230 (mmmt) REVERT: H 597 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7540 (tm-30) REVERT: H 632 THR cc_start: 0.8627 (p) cc_final: 0.8367 (t) REVERT: H 641 GLU cc_start: 0.8530 (mp0) cc_final: 0.7950 (pm20) REVERT: H 764 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: H 772 PHE cc_start: 0.8135 (m-80) cc_final: 0.7370 (m-80) REVERT: I 61 LYS cc_start: 0.9011 (tppt) cc_final: 0.8715 (tppt) REVERT: I 65 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8752 (mmmt) REVERT: I 162 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8407 (mmtp) REVERT: I 167 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5703 (t80) REVERT: I 182 ASP cc_start: 0.7743 (t0) cc_final: 0.7441 (t70) REVERT: I 194 LEU cc_start: 0.8986 (mt) cc_final: 0.8749 (mt) REVERT: I 246 LYS cc_start: 0.8959 (tppt) cc_final: 0.8678 (tppt) REVERT: I 276 GLN cc_start: 0.8795 (pp30) cc_final: 0.8510 (pp30) REVERT: I 410 LYS cc_start: 0.8228 (mmtt) cc_final: 0.8026 (mmtt) REVERT: I 503 ILE cc_start: 0.9022 (tp) cc_final: 0.8798 (tp) REVERT: I 530 LYS cc_start: 0.7697 (mptt) cc_final: 0.7312 (mptt) REVERT: I 537 GLN cc_start: 0.6927 (tm-30) cc_final: 0.5915 (tm-30) REVERT: I 542 TYR cc_start: 0.8189 (m-80) cc_final: 0.7032 (m-80) REVERT: I 764 GLN cc_start: 0.8901 (mp10) cc_final: 0.8623 (mp10) outliers start: 115 outliers final: 98 residues processed: 833 average time/residue: 0.2354 time to fit residues: 317.7421 Evaluate side-chains 854 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 748 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 368 optimal weight: 4.9990 chunk 440 optimal weight: 9.9990 chunk 3 optimal weight: 0.1980 chunk 223 optimal weight: 3.9990 chunk 482 optimal weight: 9.9990 chunk 373 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 472 optimal weight: 0.9990 chunk 464 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN F 376 ASN H 117 HIS H 567 ASN I 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108341 restraints weight = 58410.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112959 restraints weight = 28847.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115810 restraints weight = 19693.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117479 restraints weight = 15957.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118161 restraints weight = 14237.918| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38885 Z= 0.164 Angle : 0.667 15.111 52922 Z= 0.340 Chirality : 0.047 0.381 6190 Planarity : 0.004 0.073 6947 Dihedral : 4.311 36.568 5424 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.38 % Allowed : 19.70 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.24 (0.12), residues: 5043 helix: 0.56 (0.16), residues: 1298 sheet: 0.41 (0.15), residues: 1155 loop : -0.76 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 200 TYR 0.018 0.001 TYR D 542 PHE 0.034 0.001 PHE I 247 TRP 0.014 0.001 TRP H 570 HIS 0.008 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00391 (38885) covalent geometry : angle 0.66727 (52922) hydrogen bonds : bond 0.03417 ( 1346) hydrogen bonds : angle 4.74423 ( 4164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 740 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7800 (ptp-170) cc_final: 0.7177 (ptm160) REVERT: A 180 ASN cc_start: 0.8730 (t0) cc_final: 0.8501 (t0) REVERT: A 224 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 389 GLN cc_start: 0.7681 (mp10) cc_final: 0.7127 (mp10) REVERT: A 453 ASP cc_start: 0.8780 (p0) cc_final: 0.8394 (p0) REVERT: A 555 ASP cc_start: 0.7328 (t70) cc_final: 0.6952 (t70) REVERT: A 592 ARG cc_start: 0.8284 (ptt180) cc_final: 0.6429 (ptt180) REVERT: A 599 ASP cc_start: 0.7877 (t70) cc_final: 0.7650 (t70) REVERT: A 636 ARG cc_start: 0.8421 (ptp90) cc_final: 0.8099 (ptp90) REVERT: A 703 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8172 (mmtm) REVERT: A 723 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7906 (mptt) REVERT: B 190 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6983 (mt-10) REVERT: B 224 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 267 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7373 (tp30) REVERT: B 291 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7644 (mmtt) REVERT: B 335 ASP cc_start: 0.8175 (t0) cc_final: 0.7862 (t0) REVERT: B 353 ASN cc_start: 0.8458 (t0) cc_final: 0.8255 (t0) REVERT: B 446 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7750 (mmtt) REVERT: B 546 ASP cc_start: 0.8366 (t70) cc_final: 0.7916 (t0) REVERT: B 551 ASP cc_start: 0.7546 (m-30) cc_final: 0.7129 (p0) REVERT: B 563 LYS cc_start: 0.8295 (pttm) cc_final: 0.8074 (pttt) REVERT: B 594 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8259 (ttpt) REVERT: B 595 ARG cc_start: 0.8541 (ptt-90) cc_final: 0.8165 (ptt90) REVERT: B 605 VAL cc_start: 0.8610 (t) cc_final: 0.8393 (t) REVERT: B 703 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8061 (mmtm) REVERT: C 291 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8699 (mtpt) REVERT: C 326 ASN cc_start: 0.8964 (p0) cc_final: 0.8669 (p0) REVERT: C 387 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8435 (tptt) REVERT: C 441 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8383 (mm-30) REVERT: C 444 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8590 (ptpp) REVERT: C 446 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8120 (mmtt) REVERT: C 472 ASP cc_start: 0.7422 (t0) cc_final: 0.6965 (t70) REVERT: C 496 LYS cc_start: 0.9319 (ttmm) cc_final: 0.9099 (tppt) REVERT: C 497 ASP cc_start: 0.8166 (p0) cc_final: 0.7769 (p0) REVERT: C 499 ASN cc_start: 0.8637 (m-40) cc_final: 0.8252 (m-40) REVERT: C 546 ASP cc_start: 0.8252 (t0) cc_final: 0.7971 (t0) REVERT: C 560 GLN cc_start: 0.7933 (tp40) cc_final: 0.7209 (tp40) REVERT: C 582 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8739 (mmmm) REVERT: C 593 ASP cc_start: 0.8106 (t0) cc_final: 0.7550 (t0) REVERT: C 705 ASN cc_start: 0.9098 (m-40) cc_final: 0.8433 (t0) REVERT: D 265 ASP cc_start: 0.7771 (t0) cc_final: 0.6859 (t0) REVERT: D 267 GLU cc_start: 0.7940 (mp0) cc_final: 0.7468 (mp0) REVERT: D 359 ARG cc_start: 0.8499 (mtp180) cc_final: 0.7760 (mtp180) REVERT: D 389 GLN cc_start: 0.7725 (mp10) cc_final: 0.7283 (mp10) REVERT: D 434 MET cc_start: 0.8131 (ppp) cc_final: 0.7523 (ppp) REVERT: D 446 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7818 (mmmt) REVERT: D 472 ASP cc_start: 0.7640 (t0) cc_final: 0.7214 (t0) REVERT: D 479 GLU cc_start: 0.7742 (mp0) cc_final: 0.7502 (pm20) REVERT: D 496 LYS cc_start: 0.8587 (tppt) cc_final: 0.8194 (tppt) REVERT: D 497 ASP cc_start: 0.7526 (p0) cc_final: 0.6916 (p0) REVERT: D 499 ASN cc_start: 0.8615 (m110) cc_final: 0.7382 (m-40) REVERT: D 515 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7418 (mm-30) REVERT: D 587 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8570 (mtm) REVERT: D 601 ASN cc_start: 0.8277 (p0) cc_final: 0.7717 (p0) REVERT: D 703 LYS cc_start: 0.8628 (mptt) cc_final: 0.8425 (mptt) REVERT: D 722 LYS cc_start: 0.9055 (tptp) cc_final: 0.8696 (tptp) REVERT: D 727 PHE cc_start: 0.8611 (t80) cc_final: 0.7855 (t80) REVERT: E 434 MET cc_start: 0.7868 (tmm) cc_final: 0.7582 (tmm) REVERT: E 444 LYS cc_start: 0.8738 (pttm) cc_final: 0.8477 (ptpp) REVERT: E 446 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8104 (mmtt) REVERT: E 447 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7587 (tp40) REVERT: E 454 GLN cc_start: 0.8999 (mp10) cc_final: 0.8681 (mp10) REVERT: E 472 ASP cc_start: 0.8037 (t0) cc_final: 0.7479 (t0) REVERT: E 587 MET cc_start: 0.8029 (mtt) cc_final: 0.7676 (mtt) REVERT: E 599 ASP cc_start: 0.8501 (t0) cc_final: 0.8230 (t0) REVERT: E 600 ARG cc_start: 0.7599 (tpm170) cc_final: 0.6989 (tpm170) REVERT: E 602 ASN cc_start: 0.8926 (m-40) cc_final: 0.8426 (m110) REVERT: F 197 LYS cc_start: 0.8646 (tptp) cc_final: 0.8296 (tptp) REVERT: F 224 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7517 (mm-30) REVERT: F 291 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7714 (mmmm) REVERT: F 387 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9002 (ptmm) REVERT: F 388 ASN cc_start: 0.9046 (p0) cc_final: 0.8759 (p0) REVERT: F 389 GLN cc_start: 0.8091 (mp10) cc_final: 0.7711 (pm20) REVERT: F 449 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8288 (mtm-85) REVERT: F 479 GLU cc_start: 0.8243 (mp0) cc_final: 0.7930 (mp0) REVERT: F 551 ASP cc_start: 0.7693 (m-30) cc_final: 0.7197 (t70) REVERT: F 563 LYS cc_start: 0.8916 (pptt) cc_final: 0.8584 (pptt) REVERT: F 594 LYS cc_start: 0.7887 (ptpp) cc_final: 0.7481 (ptpp) REVERT: F 633 LYS cc_start: 0.9009 (tppt) cc_final: 0.8721 (tppt) REVERT: G 224 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7665 (mm-30) REVERT: G 268 ASN cc_start: 0.8520 (p0) cc_final: 0.8182 (p0) REVERT: G 434 MET cc_start: 0.7114 (tmm) cc_final: 0.6517 (tmm) REVERT: G 472 ASP cc_start: 0.7334 (t70) cc_final: 0.6525 (t0) REVERT: G 496 LYS cc_start: 0.9178 (tptt) cc_final: 0.8902 (tppt) REVERT: G 521 MET cc_start: 0.8207 (tpp) cc_final: 0.7633 (mpp) REVERT: G 563 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8599 (mmtm) REVERT: G 582 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8640 (mmmm) REVERT: G 584 ASN cc_start: 0.8394 (m-40) cc_final: 0.8058 (m-40) REVERT: G 593 ASP cc_start: 0.7999 (t0) cc_final: 0.7620 (t0) REVERT: G 600 ARG cc_start: 0.7997 (tmm-80) cc_final: 0.7534 (ttp80) REVERT: G 703 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7863 (mttp) REVERT: H 61 LYS cc_start: 0.8888 (mptt) cc_final: 0.8649 (mmtm) REVERT: H 118 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6488 (p90) REVERT: H 122 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7280 (mtmt) REVERT: H 123 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: H 248 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7865 (p0) REVERT: H 251 GLU cc_start: 0.7728 (pp20) cc_final: 0.7380 (tm-30) REVERT: H 268 TYR cc_start: 0.8910 (t80) cc_final: 0.8565 (t80) REVERT: H 273 LYS cc_start: 0.9013 (tttt) cc_final: 0.8668 (tptt) REVERT: H 446 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8427 (tp) REVERT: H 472 LYS cc_start: 0.8665 (tttp) cc_final: 0.8462 (tppt) REVERT: H 597 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7557 (tm-30) REVERT: H 632 THR cc_start: 0.8613 (p) cc_final: 0.8350 (t) REVERT: H 641 GLU cc_start: 0.8477 (mp0) cc_final: 0.7937 (pm20) REVERT: H 742 ARG cc_start: 0.9013 (tmm-80) cc_final: 0.8648 (ttp80) REVERT: H 764 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: H 772 PHE cc_start: 0.8174 (m-80) cc_final: 0.7494 (m-80) REVERT: I 37 LYS cc_start: 0.8934 (mptt) cc_final: 0.8622 (mptt) REVERT: I 61 LYS cc_start: 0.9026 (tppt) cc_final: 0.8698 (tppt) REVERT: I 65 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8744 (mmmt) REVERT: I 162 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8405 (mmtp) REVERT: I 167 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5776 (t80) REVERT: I 182 ASP cc_start: 0.7734 (t0) cc_final: 0.7428 (t70) REVERT: I 194 LEU cc_start: 0.8984 (mt) cc_final: 0.8762 (mt) REVERT: I 246 LYS cc_start: 0.8931 (tppt) cc_final: 0.8673 (tppt) REVERT: I 276 GLN cc_start: 0.8758 (pp30) cc_final: 0.8467 (pp30) REVERT: I 277 HIS cc_start: 0.7825 (t70) cc_final: 0.7482 (t70) REVERT: I 410 LYS cc_start: 0.8240 (mmtt) cc_final: 0.8018 (mmtt) REVERT: I 503 ILE cc_start: 0.9057 (tp) cc_final: 0.8828 (tp) REVERT: I 537 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6462 (tm-30) REVERT: I 542 TYR cc_start: 0.8217 (m-80) cc_final: 0.7549 (m-10) outliers start: 131 outliers final: 116 residues processed: 810 average time/residue: 0.2382 time to fit residues: 312.0111 Evaluate side-chains 859 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 734 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 587 MET Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 600 ARG Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 535 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 622 LEU Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 548 LYS Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 469 optimal weight: 8.9990 chunk 34 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS H 248 ASN H 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110978 restraints weight = 58267.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115720 restraints weight = 28468.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118640 restraints weight = 19314.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120308 restraints weight = 15593.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121310 restraints weight = 13919.306| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38885 Z= 0.120 Angle : 0.662 15.199 52922 Z= 0.335 Chirality : 0.047 0.395 6190 Planarity : 0.004 0.063 6947 Dihedral : 4.190 36.159 5424 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.76 % Allowed : 20.44 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.05 (0.12), residues: 5043 helix: 0.71 (0.16), residues: 1270 sheet: 0.48 (0.16), residues: 1091 loop : -0.58 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 200 TYR 0.016 0.001 TYR I 600 PHE 0.034 0.001 PHE I 247 TRP 0.012 0.001 TRP I 570 HIS 0.009 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00277 (38885) covalent geometry : angle 0.66203 (52922) hydrogen bonds : bond 0.03075 ( 1346) hydrogen bonds : angle 4.66712 ( 4164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 770 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7804 (ptp-170) cc_final: 0.7194 (ptm160) REVERT: A 180 ASN cc_start: 0.8750 (t0) cc_final: 0.8528 (t0) REVERT: A 204 SER cc_start: 0.8905 (t) cc_final: 0.8605 (m) REVERT: A 224 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 389 GLN cc_start: 0.7637 (mp10) cc_final: 0.7093 (mp10) REVERT: A 453 ASP cc_start: 0.8789 (p0) cc_final: 0.8371 (p0) REVERT: A 555 ASP cc_start: 0.7147 (t70) cc_final: 0.6876 (t0) REVERT: A 599 ASP cc_start: 0.8005 (t70) cc_final: 0.7751 (t70) REVERT: A 636 ARG cc_start: 0.8376 (ptp90) cc_final: 0.8018 (ptp90) REVERT: A 703 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8293 (mmtm) REVERT: A 723 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7847 (mptt) REVERT: A 725 LEU cc_start: 0.9132 (mm) cc_final: 0.8755 (pp) REVERT: B 190 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6979 (mt-10) REVERT: B 224 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 267 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7376 (tp30) REVERT: B 335 ASP cc_start: 0.8153 (t0) cc_final: 0.7876 (p0) REVERT: B 413 SER cc_start: 0.8870 (t) cc_final: 0.8556 (p) REVERT: B 434 MET cc_start: 0.8481 (ppp) cc_final: 0.8209 (ppp) REVERT: B 446 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7928 (mmtt) REVERT: B 546 ASP cc_start: 0.8345 (t70) cc_final: 0.7890 (t0) REVERT: B 551 ASP cc_start: 0.7522 (m-30) cc_final: 0.7137 (p0) REVERT: B 563 LYS cc_start: 0.8324 (pttm) cc_final: 0.8103 (pttt) REVERT: B 595 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8156 (ptt90) REVERT: B 605 VAL cc_start: 0.8474 (t) cc_final: 0.8245 (t) REVERT: B 703 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8102 (mmtm) REVERT: C 235 ASP cc_start: 0.7484 (m-30) cc_final: 0.7003 (m-30) REVERT: C 291 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8592 (mtpt) REVERT: C 326 ASN cc_start: 0.8940 (p0) cc_final: 0.8670 (p0) REVERT: C 387 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8453 (tptt) REVERT: C 441 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8358 (mm-30) REVERT: C 443 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8072 (mm-30) REVERT: C 444 LYS cc_start: 0.9061 (ptpp) cc_final: 0.8670 (ptpp) REVERT: C 446 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7874 (mmmt) REVERT: C 450 LEU cc_start: 0.9067 (mt) cc_final: 0.8822 (mp) REVERT: C 472 ASP cc_start: 0.7318 (t0) cc_final: 0.6864 (t70) REVERT: C 496 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9064 (tppt) REVERT: C 497 ASP cc_start: 0.8096 (p0) cc_final: 0.7649 (p0) REVERT: C 499 ASN cc_start: 0.8658 (m-40) cc_final: 0.8233 (m-40) REVERT: C 546 ASP cc_start: 0.8211 (t0) cc_final: 0.7930 (t0) REVERT: C 582 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8705 (mmmm) REVERT: C 593 ASP cc_start: 0.8058 (t0) cc_final: 0.7525 (t0) REVERT: C 705 ASN cc_start: 0.9131 (m-40) cc_final: 0.8790 (t0) REVERT: D 267 GLU cc_start: 0.7863 (mp0) cc_final: 0.7501 (mp0) REVERT: D 359 ARG cc_start: 0.8570 (mtp180) cc_final: 0.7901 (mtp180) REVERT: D 389 GLN cc_start: 0.7706 (mp10) cc_final: 0.7283 (mp10) REVERT: D 434 MET cc_start: 0.8157 (ppp) cc_final: 0.7397 (ppp) REVERT: D 438 GLN cc_start: 0.8491 (mp10) cc_final: 0.7975 (mp10) REVERT: D 446 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7774 (mmmt) REVERT: D 447 GLN cc_start: 0.8200 (pp30) cc_final: 0.7710 (tm-30) REVERT: D 472 ASP cc_start: 0.7496 (t0) cc_final: 0.7056 (t0) REVERT: D 496 LYS cc_start: 0.8568 (tppt) cc_final: 0.8233 (tppt) REVERT: D 497 ASP cc_start: 0.7502 (p0) cc_final: 0.6568 (p0) REVERT: D 499 ASN cc_start: 0.8594 (m110) cc_final: 0.7308 (m110) REVERT: D 515 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 543 GLN cc_start: 0.8468 (mp10) cc_final: 0.8061 (mp10) REVERT: D 586 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8715 (mttm) REVERT: D 587 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: D 703 LYS cc_start: 0.8577 (mptt) cc_final: 0.8359 (mptt) REVERT: D 722 LYS cc_start: 0.9035 (tptp) cc_final: 0.8675 (tptp) REVERT: D 727 PHE cc_start: 0.8640 (t80) cc_final: 0.7896 (t80) REVERT: E 291 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8318 (mmtt) REVERT: E 434 MET cc_start: 0.7883 (tmm) cc_final: 0.7569 (tmm) REVERT: E 444 LYS cc_start: 0.8725 (pttm) cc_final: 0.8445 (ptpp) REVERT: E 446 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7992 (mmtt) REVERT: E 447 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7608 (tp40) REVERT: E 454 GLN cc_start: 0.8980 (mp10) cc_final: 0.8637 (mp10) REVERT: E 472 ASP cc_start: 0.8005 (t0) cc_final: 0.7422 (t0) REVERT: E 587 MET cc_start: 0.7846 (mtt) cc_final: 0.7555 (mtt) REVERT: E 599 ASP cc_start: 0.8461 (t0) cc_final: 0.8183 (t0) REVERT: E 600 ARG cc_start: 0.7644 (tpm170) cc_final: 0.6886 (tpm170) REVERT: E 602 ASN cc_start: 0.8880 (m-40) cc_final: 0.8142 (m-40) REVERT: F 197 LYS cc_start: 0.8603 (tptp) cc_final: 0.8242 (tptp) REVERT: F 224 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7542 (mm-30) REVERT: F 291 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7702 (mmmm) REVERT: F 387 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9033 (ptmm) REVERT: F 388 ASN cc_start: 0.8991 (p0) cc_final: 0.8729 (p0) REVERT: F 389 GLN cc_start: 0.8125 (mp10) cc_final: 0.7727 (pm20) REVERT: F 434 MET cc_start: 0.7938 (pmm) cc_final: 0.7556 (pmm) REVERT: F 446 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8301 (mmtt) REVERT: F 449 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.8297 (mtm-85) REVERT: F 479 GLU cc_start: 0.8299 (mp0) cc_final: 0.8037 (mp0) REVERT: F 481 LEU cc_start: 0.8737 (mt) cc_final: 0.8391 (mp) REVERT: F 563 LYS cc_start: 0.8912 (pptt) cc_final: 0.8571 (pptt) REVERT: F 633 LYS cc_start: 0.8999 (tppt) cc_final: 0.7885 (tppt) REVERT: F 637 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8615 (mmtp) REVERT: G 224 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7600 (mm-30) REVERT: G 268 ASN cc_start: 0.8503 (p0) cc_final: 0.8181 (p0) REVERT: G 434 MET cc_start: 0.6943 (tmm) cc_final: 0.6490 (tmm) REVERT: G 472 ASP cc_start: 0.7125 (t70) cc_final: 0.6556 (t0) REVERT: G 496 LYS cc_start: 0.9137 (tptt) cc_final: 0.8741 (tppt) REVERT: G 521 MET cc_start: 0.8200 (tpp) cc_final: 0.7685 (mpp) REVERT: G 582 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8611 (mmmm) REVERT: G 584 ASN cc_start: 0.8382 (m-40) cc_final: 0.8063 (m-40) REVERT: G 593 ASP cc_start: 0.7871 (t0) cc_final: 0.7437 (t0) REVERT: G 600 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7476 (ttp80) REVERT: G 703 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: G 705 ASN cc_start: 0.8935 (m-40) cc_final: 0.8426 (p0) REVERT: H 61 LYS cc_start: 0.8885 (mptt) cc_final: 0.8666 (mmtm) REVERT: H 118 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6332 (p90) REVERT: H 122 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7211 (mtmt) REVERT: H 123 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8116 (mp0) REVERT: H 248 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7564 (p0) REVERT: H 251 GLU cc_start: 0.7645 (pp20) cc_final: 0.7344 (tm-30) REVERT: H 268 TYR cc_start: 0.8920 (t80) cc_final: 0.8561 (t80) REVERT: H 273 LYS cc_start: 0.8986 (tttt) cc_final: 0.8542 (ptmt) REVERT: H 446 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8395 (tp) REVERT: H 597 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 641 GLU cc_start: 0.8431 (mp0) cc_final: 0.7930 (pm20) REVERT: H 668 LEU cc_start: 0.7006 (mm) cc_final: 0.6512 (mm) REVERT: H 764 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: H 772 PHE cc_start: 0.8114 (m-80) cc_final: 0.7308 (m-80) REVERT: I 37 LYS cc_start: 0.8886 (mptt) cc_final: 0.8557 (mptt) REVERT: I 61 LYS cc_start: 0.9003 (tppt) cc_final: 0.8660 (tppt) REVERT: I 65 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8718 (mmmt) REVERT: I 162 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8346 (mmtp) REVERT: I 167 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5483 (t80) REVERT: I 182 ASP cc_start: 0.7672 (t0) cc_final: 0.7308 (t0) REVERT: I 194 LEU cc_start: 0.8964 (mt) cc_final: 0.8743 (mt) REVERT: I 246 LYS cc_start: 0.8965 (tppt) cc_final: 0.8722 (tppt) REVERT: I 263 ARG cc_start: 0.8841 (mmm160) cc_final: 0.8353 (mmm160) REVERT: I 277 HIS cc_start: 0.7960 (t70) cc_final: 0.7720 (t70) REVERT: I 410 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8019 (mmtt) REVERT: I 503 ILE cc_start: 0.9046 (tp) cc_final: 0.8814 (tp) REVERT: I 537 GLN cc_start: 0.6900 (tm-30) cc_final: 0.6438 (tm-30) REVERT: I 542 TYR cc_start: 0.8209 (m-80) cc_final: 0.7598 (m-10) outliers start: 107 outliers final: 88 residues processed: 828 average time/residue: 0.2373 time to fit residues: 317.1656 Evaluate side-chains 851 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 755 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 587 MET Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 535 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 548 LYS Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 101 optimal weight: 9.9990 chunk 234 optimal weight: 0.0670 chunk 453 optimal weight: 0.6980 chunk 278 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 457 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 214 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN E 246 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN G 246 ASN H 117 HIS H 248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110658 restraints weight = 58506.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115369 restraints weight = 28642.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118290 restraints weight = 19425.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119990 restraints weight = 15657.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120912 restraints weight = 13953.730| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38885 Z= 0.129 Angle : 0.667 15.338 52922 Z= 0.337 Chirality : 0.047 0.380 6190 Planarity : 0.004 0.065 6947 Dihedral : 4.145 36.294 5424 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.58 % Allowed : 20.91 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.04 (0.12), residues: 5043 helix: 0.76 (0.16), residues: 1262 sheet: 0.50 (0.16), residues: 1089 loop : -0.60 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 200 TYR 0.017 0.001 TYR A 598 PHE 0.035 0.001 PHE I 247 TRP 0.012 0.001 TRP H 570 HIS 0.010 0.001 HIS H 745 Details of bonding type rmsd covalent geometry : bond 0.00301 (38885) covalent geometry : angle 0.66670 (52922) hydrogen bonds : bond 0.03098 ( 1346) hydrogen bonds : angle 4.63322 ( 4164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10820.06 seconds wall clock time: 185 minutes 57.04 seconds (11157.04 seconds total)