Starting phenix.real_space_refine on Fri Mar 6 15:27:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334.map" model { file = "/net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evo_31334/03_2026/7evo_31334_neut.cif" } resolution = 2.5 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 146 5.49 5 S 115 5.16 5 C 18779 2.51 5 N 6144 2.21 5 O 6916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 202 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: 32104 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3142 Inner-chain residues flagged as termini: ['pdbres=" U H 69 "', 'pdbres=" G H 81 "'] Classifications: {'RNA': 148} Modifications used: {'5*END': 2, 'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 68, 'rna3p_pyr': 65} Link IDs: {'rna2p': 15, 'rna3p': 132} Chain breaks: 2 Chain: "1" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "2" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1210 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 22, 'TRANS': 159} Chain breaks: 4 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "3" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9247 Classifications: {'peptide': 1180} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1119} Chain breaks: 5 Chain: "4" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 664 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 140} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'TYR:plan': 8, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 10, 'ASN:plan1': 9, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 324 Chain: "5" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "6" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 504 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 117} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'PHE:plan': 10, 'ASP:plan': 6, 'GLN:plan1': 11, 'ARG:plan': 9, 'ASN:plan1': 4, 'GLU:plan': 14, 'TYR:plan': 5, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 327 Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 421 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 7, 'ARG:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 264 Chain: "C" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2103 Classifications: {'peptide': 422} Incomplete info: {'backbone_only': 293, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 1490 Unresolved non-hydrogen angles: 2092 Unresolved non-hydrogen dihedrals: 996 Unresolved non-hydrogen chiralities: 366 Planarities with less than four sites: {'GLU:plan': 51, 'GLN:plan1': 17, 'ARG:plan': 25, 'TYR:plan': 18, 'HIS:plan': 7, 'ASP:plan': 22, 'ASN:plan1': 17, 'PHE:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 844 Chain: "D" Number of atoms: 1308 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 200, 1292 Classifications: {'peptide': 200} Incomplete info: {'backbone_only': 75, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 6, 'HIS:plan': 2, 'ASP:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 216 Conformer: "B" Number of residues, atoms: 200, 1292 Classifications: {'peptide': 200} Incomplete info: {'backbone_only': 75, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 6, 'HIS:plan': 2, 'ASP:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 216 bond proxies already assigned to first conformer: 1294 Conformer: "C" Number of residues, atoms: 198, 1284 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 73, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'PHE:plan': 6, 'HIS:plan': 2, 'ASP:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 212 bond proxies already assigned to first conformer: 1294 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 2153 Classifications: {'peptide': 455} Incomplete info: {'backbone_only': 345} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 1473 Unresolved non-hydrogen angles: 2114 Unresolved non-hydrogen dihedrals: 915 Unresolved non-hydrogen chiralities: 464 Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 12, 'ARG:plan': 26, 'GLU:plan': 25, 'TRP:plan': 1, 'GLN:plan1': 15, 'HIS:plan': 8, 'TYR:plan': 12, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 648 Chain: "F" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 666 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 150} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 948 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 207 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'ARG:plan': 12, 'ASP:plan': 11, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 305 Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 685 Classifications: {'peptide': 166} Incomplete info: {'backbone_only': 149} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 6, 'ASP:plan': 7, 'GLU:plan': 9, 'PHE:plan': 13, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 337 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 372 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 83} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 10, 'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 308 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASN:plan1': 6, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'TYR:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 319 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "d" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 305 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 5, 'PHE:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 5, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 117 Chain: "e" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 341 Classifications: {'peptide': 83} Incomplete info: {'backbone_only': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 3, 'ARG:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 293 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 130 Chain: "g" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 337 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'HIS:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21417 SG CYS 6 23 102.176 109.505 166.727 1.00 30.04 S ATOM 21441 SG CYS 6 26 100.914 107.712 163.633 1.00 30.51 S ATOM 21688 SG CYS 6 58 103.665 106.007 165.658 1.00 30.08 S ATOM 21709 SG CYS 6 61 105.211 109.272 164.117 1.00 32.29 S ATOM 21330 SG CYS 6 11 113.591 95.594 160.895 1.00 25.68 S ATOM 21593 SG CYS 6 46 114.254 94.845 164.746 1.00 22.63 S ATOM 21616 SG CYS 6 49 113.117 98.173 164.109 1.00 35.44 S ATOM 21887 SG CYS 6 85 110.475 95.656 163.899 1.00 22.11 S ATOM 21468 SG CYS 6 30 96.744 96.911 161.289 1.00 19.69 S ATOM 21489 SG CYS 6 33 94.580 97.084 158.290 1.00 21.17 S ATOM 21784 SG CYS 6 72 93.485 94.690 160.756 1.00 15.15 S ATOM 21808 SG CYS 6 75 96.502 93.528 158.679 1.00 15.21 S ATOM 24277 SG CYS C 408 91.645 74.557 106.113 1.00 93.55 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ASN 2 624 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN 2 624 " occ=0.00 residue: pdb=" N ALA 2 625 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA 2 625 " occ=0.00 residue: pdb=" N HIS 2 626 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS 2 626 " occ=0.00 residue: pdb=" N LYS 2 627 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS 2 627 " occ=0.00 residue: pdb=" N AASN D 285 " occ=0.50 ... (6 atoms not shown) pdb=" O BASN D 285 " occ=0.50 residue: pdb=" N ASER D 296 " occ=0.43 ... (6 atoms not shown) pdb=" O BSER D 296 " occ=0.57 residue: pdb=" N ASER D 318 " occ=0.45 ... (10 atoms not shown) pdb=" O CSER D 318 " occ=0.41 Time building chain proxies: 6.85, per 1000 atoms: 0.21 Number of scatterers: 32104 At special positions: 0 Unit cell: (169.572, 178.268, 239.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 115 16.00 P 146 15.00 O 6916 8.00 N 6144 7.00 C 18779 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: 2.36 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 85 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 425 " pdb="ZN ZN C1000 " - pdb=" ND1 HIS C 431 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 408 " Number of angles added : 18 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 45 sheets defined 38.5% alpha, 19.3% beta 33 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain '1' and resid 491 through 499 removed outlier: 3.614A pdb=" N ARG 1 495 " --> pdb=" O GLU 1 491 " (cutoff:3.500A) Processing helix chain '1' and resid 499 through 506 Processing helix chain '1' and resid 508 through 527 removed outlier: 4.761A pdb=" N ARG 1 524 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU 1 525 " --> pdb=" O ASP 1 521 " (cutoff:3.500A) Processing helix chain '1' and resid 527 through 540 Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 545 through 563 removed outlier: 3.544A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU 1 563 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 569 No H-bonds generated for 'chain '1' and resid 567 through 569' Processing helix chain '1' and resid 570 through 579 Processing helix chain '1' and resid 586 through 604 Processing helix chain '1' and resid 605 through 614 Processing helix chain '1' and resid 615 through 618 removed outlier: 3.816A pdb=" N ASP 1 618 " --> pdb=" O PRO 1 615 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 615 through 618' Processing helix chain '1' and resid 621 through 640 removed outlier: 3.518A pdb=" N ARG 1 625 " --> pdb=" O ASP 1 621 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN 1 626 " --> pdb=" O GLU 1 622 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR 1 627 " --> pdb=" O TYR 1 623 " (cutoff:3.500A) Processing helix chain '1' and resid 644 through 652 Processing helix chain '1' and resid 657 through 676 removed outlier: 4.011A pdb=" N ARG 1 661 " --> pdb=" O SER 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 677 through 681 removed outlier: 3.875A pdb=" N LEU 1 680 " --> pdb=" O CYS 1 677 " (cutoff:3.500A) Proline residue: 1 681 - end of helix No H-bonds generated for 'chain '1' and resid 677 through 681' Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 692 through 696 removed outlier: 3.758A pdb=" N VAL 1 695 " --> pdb=" O HIS 1 692 " (cutoff:3.500A) Processing helix chain '1' and resid 698 through 717 Processing helix chain '1' and resid 727 through 738 Processing helix chain '1' and resid 740 through 754 Processing helix chain '1' and resid 755 through 757 No H-bonds generated for 'chain '1' and resid 755 through 757' Processing helix chain '1' and resid 758 through 777 removed outlier: 3.653A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) Processing helix chain '1' and resid 781 through 796 removed outlier: 3.544A pdb=" N LYS 1 785 " --> pdb=" O ASP 1 781 " (cutoff:3.500A) Processing helix chain '1' and resid 802 through 810 Processing helix chain '1' and resid 810 through 818 Processing helix chain '1' and resid 820 through 826 removed outlier: 3.605A pdb=" N ALA 1 824 " --> pdb=" O GLN 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 829 through 845 removed outlier: 3.833A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 845 through 855 removed outlier: 4.203A pdb=" N ILE 1 849 " --> pdb=" O GLY 1 845 " (cutoff:3.500A) Processing helix chain '1' and resid 861 through 879 removed outlier: 3.517A pdb=" N ARG 1 865 " --> pdb=" O ALA 1 861 " (cutoff:3.500A) Processing helix chain '1' and resid 885 through 902 Processing helix chain '1' and resid 907 through 922 removed outlier: 3.891A pdb=" N LEU 1 911 " --> pdb=" O ASP 1 907 " (cutoff:3.500A) Processing helix chain '1' and resid 923 through 925 No H-bonds generated for 'chain '1' and resid 923 through 925' Processing helix chain '1' and resid 927 through 942 removed outlier: 4.429A pdb=" N ASN 1 942 " --> pdb=" O TRP 1 938 " (cutoff:3.500A) Processing helix chain '1' and resid 945 through 965 removed outlier: 3.588A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS 1 965 " --> pdb=" O VAL 1 961 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 981 Processing helix chain '1' and resid 986 through 1004 Processing helix chain '1' and resid 1012 through 1021 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1022 through 1026 removed outlier: 3.534A pdb=" N LYS 11025 " --> pdb=" O PRO 11022 " (cutoff:3.500A) Processing helix chain '1' and resid 1028 through 1046 Processing helix chain '1' and resid 1047 through 1050 removed outlier: 3.937A pdb=" N VAL 11050 " --> pdb=" O ALA 11047 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1047 through 1050' Processing helix chain '1' and resid 1051 through 1063 Processing helix chain '1' and resid 1064 through 1068 removed outlier: 3.623A pdb=" N LYS 11067 " --> pdb=" O GLU 11064 " (cutoff:3.500A) Processing helix chain '1' and resid 1070 through 1089 Processing helix chain '1' and resid 1089 through 1103 removed outlier: 4.186A pdb=" N VAL 11093 " --> pdb=" O GLY 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1105 through 1123 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1128 through 1136 removed outlier: 3.575A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) Processing helix chain '1' and resid 1143 through 1159 Processing helix chain '1' and resid 1160 through 1164 removed outlier: 3.871A pdb=" N ASP 11164 " --> pdb=" O MET 11161 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1178 removed outlier: 3.697A pdb=" N VAL 11169 " --> pdb=" O TYR 11165 " (cutoff:3.500A) Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1181 through 1199 removed outlier: 3.607A pdb=" N ARG 11185 " --> pdb=" O ASP 11181 " (cutoff:3.500A) Processing helix chain '1' and resid 1204 through 1216 removed outlier: 3.604A pdb=" N LEU 11208 " --> pdb=" O CYS 11204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Processing helix chain '1' and resid 1217 through 1221 removed outlier: 4.211A pdb=" N PHE 11220 " --> pdb=" O PRO 11217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU 11221 " --> pdb=" O ASN 11218 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1217 through 1221' Processing helix chain '1' and resid 1223 through 1241 removed outlier: 3.604A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) Processing helix chain '1' and resid 1242 through 1251 removed outlier: 3.725A pdb=" N MET 11246 " --> pdb=" O GLY 11242 " (cutoff:3.500A) Processing helix chain '1' and resid 1252 through 1254 No H-bonds generated for 'chain '1' and resid 1252 through 1254' Processing helix chain '1' and resid 1258 through 1275 removed outlier: 3.687A pdb=" N GLY 11275 " --> pdb=" O SER 11271 " (cutoff:3.500A) Processing helix chain '1' and resid 1278 through 1283 Processing helix chain '1' and resid 1298 through 1302 Processing helix chain '2' and resid 461 through 469 removed outlier: 3.612A pdb=" N LEU 2 468 " --> pdb=" O GLU 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 475 removed outlier: 3.741A pdb=" N VAL 2 474 " --> pdb=" O ARG 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 482 removed outlier: 4.027A pdb=" N VAL 2 480 " --> pdb=" O MET 2 477 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 2 482 " --> pdb=" O ASP 2 479 " (cutoff:3.500A) Processing helix chain '2' and resid 484 through 493 Processing helix chain '2' and resid 525 through 530 removed outlier: 3.967A pdb=" N LYS 2 529 " --> pdb=" O PRO 2 525 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 578 Processing helix chain '2' and resid 610 through 618 removed outlier: 3.565A pdb=" N GLY 2 618 " --> pdb=" O ARG 2 614 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 640 removed outlier: 3.713A pdb=" N MET 2 636 " --> pdb=" O TRP 2 632 " (cutoff:3.500A) Processing helix chain '3' and resid 190 through 194 Processing helix chain '3' and resid 429 through 432 removed outlier: 3.522A pdb=" N ARG 3 432 " --> pdb=" O ARG 3 429 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 429 through 432' Processing helix chain '3' and resid 808 through 825 removed outlier: 3.673A pdb=" N GLU 3 825 " --> pdb=" O GLU 3 821 " (cutoff:3.500A) Processing helix chain '3' and resid 838 through 843 Processing helix chain '3' and resid 848 through 853 Processing helix chain '3' and resid 1134 through 1152 removed outlier: 3.576A pdb=" N HIS 31138 " --> pdb=" O SER 31134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1159 through 1164 Processing helix chain '3' and resid 1176 through 1180 Processing helix chain '3' and resid 1181 through 1185 Processing helix chain '3' and resid 1186 through 1195 Processing helix chain '3' and resid 1200 through 1216 removed outlier: 3.643A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR 31215 " --> pdb=" O ILE 31211 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 33 removed outlier: 3.700A pdb=" N TRP 4 30 " --> pdb=" O GLU 4 26 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 74 removed outlier: 3.511A pdb=" N ALA 4 67 " --> pdb=" O SER 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 112 through 121 Processing helix chain '4' and resid 151 through 161 removed outlier: 3.665A pdb=" N SER 4 155 " --> pdb=" O SER 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 46 Processing helix chain '5' and resid 46 through 57 removed outlier: 3.617A pdb=" N LEU 5 50 " --> pdb=" O HIS 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 73 removed outlier: 4.161A pdb=" N LEU 5 73 " --> pdb=" O MET 5 69 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 55 Processing helix chain '6' and resid 73 through 78 Processing helix chain '6' and resid 79 through 83 removed outlier: 4.076A pdb=" N ASP 6 83 " --> pdb=" O LYS 6 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.896A pdb=" N GLN A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 Processing helix chain 'A' and resid 235 through 272 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'C' and resid 5 through 28 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.660A pdb=" N ASP C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 4.717A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.557A pdb=" N MET C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.561A pdb=" N VAL C 128 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 181 through 201 removed outlier: 4.001A pdb=" N TYR C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.105A pdb=" N GLY C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.110A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.533A pdb=" N LYS C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.512A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 3.584A pdb=" N LYS C 398 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.667A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.095A pdb=" N LEU C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.624A pdb=" N ALA C 447 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 470 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.566A pdb=" N PHE D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.875A pdb=" N VAL D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.821A pdb=" N LYS D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'E' and resid 153 through 178 Processing helix chain 'E' and resid 226 through 243 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.805A pdb=" N LEU E 355 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.602A pdb=" N GLN E 376 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS E 377 " --> pdb=" O TRP E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 377' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 396 through 408 Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 421 through 437 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 454 through 469 Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.599A pdb=" N GLN E 488 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 530 through 535 Processing helix chain 'E' and resid 539 through 549 Processing helix chain 'E' and resid 564 through 572 Processing helix chain 'E' and resid 603 through 615 removed outlier: 4.196A pdb=" N LEU E 607 " --> pdb=" O GLU E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 642 Processing helix chain 'E' and resid 654 through 668 Processing helix chain 'E' and resid 699 through 709 removed outlier: 3.750A pdb=" N TYR E 703 " --> pdb=" O HIS E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 36 through 40 removed outlier: 4.208A pdb=" N ALA F 39 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 40 " --> pdb=" O LEU F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 40' Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.527A pdb=" N ALA F 86 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.722A pdb=" N ASP F 105 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Proline residue: F 108 - end of helix removed outlier: 3.603A pdb=" N SER F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 61 through 72 removed outlier: 3.511A pdb=" N SER G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 196 through 207 Processing helix chain 'a' and resid 20 through 27 Processing helix chain 'a' and resid 28 through 38 removed outlier: 3.699A pdb=" N LEU a 32 " --> pdb=" O PRO a 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER a 35 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN a 38 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 14 Processing helix chain 'c' and resid 16 through 28 Processing helix chain 'e' and resid 4 through 13 Processing helix chain 'g' and resid 2 through 9 removed outlier: 3.873A pdb=" N PHE g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain '2' and resid 648 through 649 Processing sheet with id=AA2, first strand: chain '3' and resid 1101 through 1108 removed outlier: 3.745A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE 31128 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR 3 7 " --> pdb=" O ILE 31128 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 31130 " --> pdb=" O ASN 3 5 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN 3 5 " --> pdb=" O VAL 31130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 16 through 20 removed outlier: 3.667A pdb=" N PHE 3 16 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 3 54 " --> pdb=" O LEU 3 40 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 62 through 68 removed outlier: 4.401A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE 3 87 " --> pdb=" O GLN 3 104 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN 3 104 " --> pdb=" O ILE 3 87 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE 3 89 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET 3 98 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA6, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA7, first strand: chain '3' and resid 165 through 173 removed outlier: 5.654A pdb=" N VAL 3 167 " --> pdb=" O MET 3 187 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N MET 3 187 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS 3 169 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU 3 208 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER 3 225 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE 3 210 " --> pdb=" O LYS 3 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS 3 219 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 232 through 237 removed outlier: 4.493A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR 3 255 " --> pdb=" O SER 3 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 273 through 274 removed outlier: 6.353A pdb=" N ARG 3 273 " --> pdb=" O PHE 3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 287 through 294 removed outlier: 6.874A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE 3 310 " --> pdb=" O PHE 3 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 336 through 342 removed outlier: 3.689A pdb=" N ALA 3 338 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS 3 356 " --> pdb=" O GLU 3 400 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU 3 400 " --> pdb=" O HIS 3 356 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU 3 358 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 407 through 413 Processing sheet with id=AB4, first strand: chain '3' and resid 444 through 449 removed outlier: 6.379A pdb=" N ILE 3 764 " --> pdb=" O MET 3 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 461 through 462 removed outlier: 3.502A pdb=" N VAL 3 462 " --> pdb=" O TYR 3 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 507 through 510 removed outlier: 3.822A pdb=" N GLN 3 518 " --> pdb=" O ARG 3 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3' and resid 546 through 548 removed outlier: 4.332A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 3 564 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 587 through 592 removed outlier: 3.618A pdb=" N SER 3 591 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA 3 606 " --> pdb=" O SER 3 591 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '3' and resid 637 through 643 removed outlier: 4.268A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS 3 641 " --> pdb=" O ASN 3 666 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 3 674 " --> pdb=" O THR 3 689 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 3 689 " --> pdb=" O LEU 3 674 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 700 through 706 removed outlier: 3.667A pdb=" N VAL 3 712 " --> pdb=" O SER 3 722 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 785 through 790 removed outlier: 7.111A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER 3 864 " --> pdb=" O GLN 3 881 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLN 3 881 " --> pdb=" O SER 3 864 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE 3 866 " --> pdb=" O LEU 3 879 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 3 879 " --> pdb=" O ILE 3 866 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL 3 868 " --> pdb=" O LEU 3 877 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 886 through 894 removed outlier: 6.605A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 953 through 955 removed outlier: 6.824A pdb=" N LEU 3 967 " --> pdb=" O GLU 3 982 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU 3 982 " --> pdb=" O LEU 3 967 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL 3 969 " --> pdb=" O LYS 3 980 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 990 through 996 removed outlier: 3.731A pdb=" N GLY 3 992 " --> pdb=" O SER 31003 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE 31009 " --> pdb=" O ASP 31026 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP 31026 " --> pdb=" O PHE 31009 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP 31011 " --> pdb=" O PHE 31024 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 1033 through 1038 removed outlier: 4.373A pdb=" N THR 31035 " --> pdb=" O ALA 31047 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET 31093 " --> pdb=" O VAL 31055 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 39 through 43 Processing sheet with id=AC8, first strand: chain '4' and resid 131 through 132 removed outlier: 3.539A pdb=" N LYS 4 131 " --> pdb=" O PHE 4 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 9 through 10 removed outlier: 3.533A pdb=" N ILE 6 9 " --> pdb=" O VAL 6 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 18 through 19 removed outlier: 4.133A pdb=" N ALA 6 18 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 21 through 22 Processing sheet with id=AD3, first strand: chain '6' and resid 39 through 42 removed outlier: 6.227A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 118 through 121 removed outlier: 4.005A pdb=" N LYS B 118 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 148 through 153 removed outlier: 4.030A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 282 through 283 removed outlier: 4.093A pdb=" N ALA C 282 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 406 through 408 removed outlier: 3.619A pdb=" N TYR C 414 " --> pdb=" O CYS C 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 170 through 174 removed outlier: 4.596A pdb=" N ASP D 183 " --> pdb=" O TYR D 173 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 301 through 306 Processing sheet with id=AE1, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.594A pdb=" N ARG D 340 " --> pdb=" O PHE D 337 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 362 through 363 removed outlier: 6.008A pdb=" N VAL E 526 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE E 559 " --> pdb=" O VAL E 526 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU E 528 " --> pdb=" O PHE E 559 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL E 449 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP E 529 " --> pdb=" O VAL E 449 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N MET E 451 " --> pdb=" O ASP E 529 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 593 through 599 removed outlier: 6.083A pdb=" N GLU E 594 " --> pdb=" O ALA E 719 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR E 721 " --> pdb=" O GLU E 594 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN E 596 " --> pdb=" O THR E 721 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE E 723 " --> pdb=" O GLN E 596 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE E 598 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 691 " --> pdb=" O TYR E 720 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE E 722 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN E 693 " --> pdb=" O PHE E 722 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 622 " --> pdb=" O LEU E 673 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA E 675 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 624 " --> pdb=" O ALA E 675 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET E 647 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 13 through 16 removed outlier: 4.136A pdb=" N ALA F 13 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG F 22 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP F 48 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 24 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE F 47 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE6, first strand: chain 'G' and resid 40 through 45 Processing sheet with id=AE7, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AE8, first strand: chain 'G' and resid 177 through 181 removed outlier: 3.651A pdb=" N GLU G 179 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 56 through 57 removed outlier: 3.840A pdb=" N GLN e 60 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS d 20 " --> pdb=" O ILE d 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU d 70 " --> pdb=" O SER d 18 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER d 18 " --> pdb=" O LEU d 70 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA d 72 " --> pdb=" O LYS d 16 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS d 16 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS d 26 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE d 30 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU d 44 " --> pdb=" O ILE d 30 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY d 58 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL d 46 " --> pdb=" O ASN d 56 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN d 56 " --> pdb=" O VAL d 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET d 48 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN d 54 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET d 59 " --> pdb=" O SER c 89 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER c 89 " --> pdb=" O MET d 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU c 86 " --> pdb=" O TRP c 34 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU c 35 " --> pdb=" O MET c 41 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N MET c 41 " --> pdb=" O LEU c 35 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS c 46 " --> pdb=" O ASP c 60 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP c 60 " --> pdb=" O CYS c 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL c 57 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET c 78 " --> pdb=" O VAL c 57 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP c 59 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG c 76 " --> pdb=" O ASP c 59 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA c 61 " --> pdb=" O LEU c 74 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG c 76 " --> pdb=" O GLY b 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY b 74 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE b 72 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET b 27 " --> pdb=" O LEU b 23 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR b 32 " --> pdb=" O ASN b 46 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN b 46 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL b 34 " --> pdb=" O LEU b 44 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU b 44 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL b 36 " --> pdb=" O MET b 42 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET b 42 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN b 43 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL b 62 " --> pdb=" O GLN b 43 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA b 45 " --> pdb=" O GLY b 60 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY b 60 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR b 47 " --> pdb=" O HIS b 58 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS b 58 " --> pdb=" O THR b 47 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU b 49 " --> pdb=" O SER b 56 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG a 55 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN a 69 " --> pdb=" O ARG a 55 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS a 57 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU a 67 " --> pdb=" O LYS a 57 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER a 97 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS a 71 " --> pdb=" O TYR a 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR a 95 " --> pdb=" O LYS a 71 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET a 73 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP a 93 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR a 75 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN a 91 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS a 98 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU g 70 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU g 13 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL g 25 " --> pdb=" O MET g 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET g 45 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY g 27 " --> pdb=" O VAL g 43 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL g 43 " --> pdb=" O GLY g 27 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS g 41 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS g 39 " --> pdb=" O SER g 59 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER g 59 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS g 41 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR g 57 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR g 57 " --> pdb=" O VAL f 82 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL f 82 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER f 79 " --> pdb=" O ILE f 20 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR f 15 " --> pdb=" O PHE f 31 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR f 30 " --> pdb=" O ASP f 44 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP f 44 " --> pdb=" O THR f 30 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE f 41 " --> pdb=" O LEU f 72 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU f 72 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N CYS f 43 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL f 70 " --> pdb=" O CYS f 43 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU f 47 " --> pdb=" O VAL f 66 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL f 66 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU f 69 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS e 31 " --> pdb=" O ASN e 45 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN e 45 " --> pdb=" O LYS e 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE e 33 " --> pdb=" O MET e 43 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET e 43 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA e 35 " --> pdb=" O CYS e 41 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS e 41 " --> pdb=" O ALA e 35 " (cutoff:3.500A) 1604 hydrogen bonds defined for protein. 4558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 8.12 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6688 1.33 - 1.45: 8396 1.45 - 1.57: 17395 1.57 - 1.69: 288 1.69 - 1.81: 177 Bond restraints: 32944 Sorted by residual: bond pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.21e+01 bond pdb=" C16 9B0 11500 " pdb=" C17 9B0 11500 " ideal model delta sigma weight residual 1.450 1.317 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O3' C H 45 " pdb=" P U H 46 " ideal model delta sigma weight residual 1.607 1.521 0.086 1.50e-02 4.44e+03 3.26e+01 bond pdb=" N GLU D 252 " pdb=" CA GLU D 252 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.44e+01 bond pdb=" C ALA E 178 " pdb=" O ALA E 178 " ideal model delta sigma weight residual 1.231 1.326 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 32939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 44307 3.64 - 7.28: 193 7.28 - 10.92: 19 10.92 - 14.56: 6 14.56 - 18.20: 2 Bond angle restraints: 44527 Sorted by residual: angle pdb=" O2' C H 28 " pdb=" C2' C H 28 " pdb=" C1' C H 28 " ideal model delta sigma weight residual 108.40 90.20 18.20 1.50e+00 4.44e-01 1.47e+02 angle pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " pdb=" CA PRO 5 79 " ideal model delta sigma weight residual 119.84 134.32 -14.48 1.25e+00 6.40e-01 1.34e+02 angle pdb=" C4' G H 42 " pdb=" C3' G H 42 " pdb=" O3' G H 42 " ideal model delta sigma weight residual 113.00 127.69 -14.69 1.50e+00 4.44e-01 9.59e+01 angle pdb=" C2' C H 28 " pdb=" C1' C H 28 " pdb=" N1 C H 28 " ideal model delta sigma weight residual 112.00 98.99 13.01 1.50e+00 4.44e-01 7.52e+01 angle pdb=" C3' U H 27 " pdb=" C2' U H 27 " pdb=" C1' U H 27 " ideal model delta sigma weight residual 101.30 107.12 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 44522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 16469 35.55 - 71.09: 819 71.09 - 106.64: 71 106.64 - 142.18: 14 142.18 - 177.73: 5 Dihedral angle restraints: 17378 sinusoidal: 7711 harmonic: 9667 Sorted by residual: dihedral pdb=" O4' U H 47 " pdb=" C1' U H 47 " pdb=" N1 U H 47 " pdb=" C2 U H 47 " ideal model delta sinusoidal sigma weight residual 200.00 45.27 154.73 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" CA GLU 3 136 " pdb=" C GLU 3 136 " pdb=" N LYS 3 137 " pdb=" CA LYS 3 137 " ideal model delta harmonic sigma weight residual 180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ILE 3 996 " pdb=" C ILE 3 996 " pdb=" N GLY 3 997 " pdb=" CA GLY 3 997 " ideal model delta harmonic sigma weight residual -180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3906 0.136 - 0.271: 35 0.271 - 0.407: 4 0.407 - 0.543: 0 0.543 - 0.678: 1 Chirality restraints: 3946 Sorted by residual: chirality pdb=" C3' G H 42 " pdb=" C4' G H 42 " pdb=" O3' G H 42 " pdb=" C2' G H 42 " both_signs ideal model delta sigma weight residual False -2.48 -1.80 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C3' U H 43 " pdb=" C4' U H 43 " pdb=" O3' U H 43 " pdb=" C2' U H 43 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA TYR C 394 " pdb=" N TYR C 394 " pdb=" C TYR C 394 " pdb=" CB TYR C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 3943 not shown) Planarity restraints: 5945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U H 43 " -0.025 2.00e-02 2.50e+03 9.03e-02 1.83e+02 pdb=" N1 U H 43 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U H 43 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U H 43 " -0.046 2.00e-02 2.50e+03 pdb=" N3 U H 43 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U H 43 " 0.054 2.00e-02 2.50e+03 pdb=" O4 U H 43 " 0.039 2.00e-02 2.50e+03 pdb=" C5 U H 43 " -0.214 2.00e-02 2.50e+03 pdb=" C6 U H 43 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9B0 11500 " -0.109 2.00e-02 2.50e+03 1.06e-01 1.11e+02 pdb=" C11 9B0 11500 " 0.106 2.00e-02 2.50e+03 pdb=" C8 9B0 11500 " 0.105 2.00e-02 2.50e+03 pdb=" C9 9B0 11500 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 393 " -0.045 2.00e-02 2.50e+03 8.99e-02 8.09e+01 pdb=" C PRO C 393 " 0.155 2.00e-02 2.50e+03 pdb=" O PRO C 393 " -0.060 2.00e-02 2.50e+03 pdb=" N TYR C 394 " -0.051 2.00e-02 2.50e+03 ... (remaining 5942 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 216 2.62 - 3.19: 25362 3.19 - 3.76: 46481 3.76 - 4.33: 63009 4.33 - 4.90: 99665 Nonbonded interactions: 234733 Sorted by model distance: nonbonded pdb=" OD1 ASP E 226 " pdb=" CD PRO E 227 " model vdw 2.045 3.440 nonbonded pdb=" O LEU C 402 " pdb=" ND2 ASN C 403 " model vdw 2.165 3.120 nonbonded pdb=" O LYS 3 343 " pdb=" OG1 THR 3 344 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP 6 27 " pdb=" OG SER 6 67 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN 31183 " pdb=" OG SER 31205 " model vdw 2.217 3.040 ... (remaining 234728 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 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 : 0.005 0.308 32959 Z= 0.271 Angle : 0.812 29.253 44545 Z= 0.477 Chirality : 0.049 0.678 3946 Planarity : 0.006 0.106 5945 Dihedral : 18.396 177.728 12442 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 5.50 % Allowed : 21.66 % Favored : 72.83 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.10), residues: 4597 helix: -2.04 (0.10), residues: 1618 sheet: -1.07 (0.16), residues: 999 loop : -2.43 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 166 TYR 0.018 0.001 TYR C 394 PHE 0.018 0.002 PHE D 168 TRP 0.034 0.002 TRP C 395 HIS 0.012 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00417 (32944) covalent geometry : angle 0.77358 (44527) hydrogen bonds : bond 0.15673 ( 1684) hydrogen bonds : angle 6.57777 ( 4730) metal coordination : bond 0.14014 ( 15) metal coordination : angle 12.27296 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 423 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6756 (mmt90) REVERT: 1 655 LYS cc_start: 0.7741 (mmpt) cc_final: 0.7524 (mptt) REVERT: 1 835 ASP cc_start: 0.7521 (m-30) cc_final: 0.7318 (m-30) REVERT: 1 883 ASP cc_start: 0.5846 (p0) cc_final: 0.5156 (t0) REVERT: 1 890 GLU cc_start: 0.6954 (tt0) cc_final: 0.6669 (tp30) REVERT: 1 926 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6411 (mmmm) REVERT: 1 929 LEU cc_start: 0.7498 (mt) cc_final: 0.7254 (tt) REVERT: 1 962 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6073 (ttm) REVERT: 1 967 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4202 (tp30) REVERT: 1 1037 ASP cc_start: 0.7941 (m-30) cc_final: 0.7521 (m-30) REVERT: 1 1053 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6713 (ttt180) REVERT: 1 1056 MET cc_start: 0.8357 (mmm) cc_final: 0.8078 (mmm) REVERT: 1 1160 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: 1 1161 MET cc_start: 0.8315 (ttm) cc_final: 0.7827 (mtp) REVERT: 3 114 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8634 (ttp-170) REVERT: 3 191 GLU cc_start: 0.7116 (pm20) cc_final: 0.6705 (pt0) REVERT: 3 316 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: 3 326 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8159 (mtt180) REVERT: 3 377 MET cc_start: 0.8437 (mtt) cc_final: 0.7966 (mtp) REVERT: 3 573 GLN cc_start: 0.2320 (OUTLIER) cc_final: 0.1860 (mm-40) REVERT: 3 583 MET cc_start: 0.2905 (mtm) cc_final: 0.2205 (tmm) REVERT: 3 630 MET cc_start: 0.3854 (ttm) cc_final: 0.3177 (tpp) REVERT: 3 1143 HIS cc_start: 0.7826 (m90) cc_final: 0.7363 (t-90) REVERT: 3 1188 ASN cc_start: 0.6987 (p0) cc_final: 0.6656 (p0) REVERT: 3 1189 LYS cc_start: 0.8053 (mttm) cc_final: 0.7810 (mmtt) REVERT: C 403 ASN cc_start: 0.7206 (p0) cc_final: 0.6841 (p0) REVERT: C 414 TYR cc_start: 0.7080 (t80) cc_final: 0.6799 (t80) REVERT: D 202 ASP cc_start: 0.7369 (t0) cc_final: 0.7010 (t70) REVERT: D 203 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6497 (mt-10) REVERT: D 204 ASP cc_start: 0.7154 (t70) cc_final: 0.6870 (t70) REVERT: D 242 MET cc_start: 0.6155 (mmm) cc_final: 0.5797 (tmm) REVERT: E 205 ASP cc_start: 0.4762 (t0) cc_final: 0.4261 (p0) outliers start: 125 outliers final: 46 residues processed: 530 average time/residue: 0.7297 time to fit residues: 453.9782 Evaluate side-chains 403 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 349 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 956 SER Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 351 SER Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.2980 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 50.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 506 ASN 1 534 GLN 1 804 ASN 11007 HIS 11032 GLN 11107 GLN 11144 GLN 11194 HIS 11252 GLN 11256 HIS 11293 ASN 2 458 ASN 2 467 GLN 2 490 HIS 3 46 ASN 3 93 GLN 3 219 HIS 3 264 GLN 3 363 HIS 3 480 ASN 3 594 ASN 3 612 ASN 3 776 GLN 3 796 ASN 3 805 ASN 3 846 ASN 3 870 ASN 3 916 ASN 3 941 HIS 3 983 ASN 31017 ASN 31052 ASN C 400 HIS C 403 ASN D 179 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.256401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.200976 restraints weight = 68949.706| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 6.13 r_work: 0.3296 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32959 Z= 0.141 Angle : 0.605 12.723 44545 Z= 0.310 Chirality : 0.043 0.175 3946 Planarity : 0.005 0.062 5945 Dihedral : 15.322 157.178 7343 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 6.52 % Allowed : 22.63 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.11), residues: 4597 helix: 0.06 (0.12), residues: 1622 sheet: -0.56 (0.16), residues: 1002 loop : -1.91 (0.12), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 250 TYR 0.019 0.002 TYR D 136 PHE 0.018 0.002 PHE D 168 TRP 0.013 0.001 TRP C 395 HIS 0.009 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00308 (32944) covalent geometry : angle 0.59908 (44527) hydrogen bonds : bond 0.04488 ( 1684) hydrogen bonds : angle 4.59737 ( 4730) metal coordination : bond 0.00864 ( 15) metal coordination : angle 4.41295 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 366 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 503 LYS cc_start: 0.5776 (tttp) cc_final: 0.5122 (mmtp) REVERT: 1 554 LYS cc_start: 0.7401 (ttmm) cc_final: 0.7108 (mmtp) REVERT: 1 558 ARG cc_start: 0.7337 (mmp80) cc_final: 0.6899 (mmt90) REVERT: 1 564 ASP cc_start: 0.7131 (m-30) cc_final: 0.6882 (m-30) REVERT: 1 566 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7227 (mp) REVERT: 1 570 TYR cc_start: 0.7871 (m-80) cc_final: 0.7655 (m-10) REVERT: 1 656 LYS cc_start: 0.7314 (mmtp) cc_final: 0.6882 (mmtt) REVERT: 1 835 ASP cc_start: 0.7937 (m-30) cc_final: 0.7605 (m-30) REVERT: 1 839 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: 1 883 ASP cc_start: 0.6212 (p0) cc_final: 0.5631 (t0) REVERT: 1 890 GLU cc_start: 0.7019 (tt0) cc_final: 0.6599 (tp30) REVERT: 1 926 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6646 (mmmm) REVERT: 1 957 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7240 (mtm-85) REVERT: 1 967 GLU cc_start: 0.4747 (OUTLIER) cc_final: 0.4161 (tp30) REVERT: 1 1007 HIS cc_start: 0.3332 (OUTLIER) cc_final: 0.2786 (p-80) REVERT: 1 1037 ASP cc_start: 0.8544 (m-30) cc_final: 0.8214 (m-30) REVERT: 1 1056 MET cc_start: 0.8980 (mmm) cc_final: 0.8739 (mmm) REVERT: 1 1135 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: 1 1160 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: 1 1161 MET cc_start: 0.9093 (ttm) cc_final: 0.8857 (ttm) REVERT: 2 502 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7676 (ptp-170) REVERT: 2 572 HIS cc_start: 0.5123 (OUTLIER) cc_final: 0.3953 (t70) REVERT: 2 575 PHE cc_start: 0.3860 (t80) cc_final: 0.3027 (t80) REVERT: 3 178 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: 3 316 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: 3 326 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8607 (mtt180) REVERT: 3 377 MET cc_start: 0.8569 (mtt) cc_final: 0.8161 (mtp) REVERT: 3 573 GLN cc_start: 0.2643 (OUTLIER) cc_final: 0.2142 (mm-40) REVERT: 3 583 MET cc_start: 0.3249 (mtm) cc_final: 0.2006 (tmm) REVERT: 3 630 MET cc_start: 0.3519 (ttm) cc_final: 0.2896 (tpp) REVERT: 3 715 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6950 (mmm) REVERT: 3 809 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: 3 821 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: 3 1143 HIS cc_start: 0.8751 (m90) cc_final: 0.8044 (t-90) REVERT: 3 1188 ASN cc_start: 0.7728 (p0) cc_final: 0.7475 (p0) REVERT: 6 25 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7327 (pttm) REVERT: 6 48 GLU cc_start: 0.7960 (pp20) cc_final: 0.7756 (pp20) REVERT: D 143 ASP cc_start: 0.5168 (p0) cc_final: 0.4615 (p0) REVERT: D 147 ASP cc_start: 0.7069 (m-30) cc_final: 0.6843 (m-30) REVERT: D 148 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5997 (pp20) REVERT: D 153 MET cc_start: 0.8544 (mmm) cc_final: 0.8145 (mmp) REVERT: D 202 ASP cc_start: 0.7855 (t0) cc_final: 0.7398 (t70) REVERT: D 203 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6578 (mt-10) REVERT: D 204 ASP cc_start: 0.7287 (t70) cc_final: 0.6949 (t70) REVERT: D 242 MET cc_start: 0.6343 (mmm) cc_final: 0.6006 (tmm) REVERT: E 196 LYS cc_start: 0.3863 (OUTLIER) cc_final: 0.3240 (mmmm) REVERT: E 205 ASP cc_start: 0.4580 (t0) cc_final: 0.3888 (p0) outliers start: 148 outliers final: 61 residues processed: 482 average time/residue: 0.6982 time to fit residues: 397.7033 Evaluate side-chains 428 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 350 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 556 ILE Chi-restraints excluded: chain 1 residue 566 LEU Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1007 HIS Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 476 GLU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 715 MET Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 864 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 231 optimal weight: 50.0000 chunk 38 optimal weight: 0.9990 chunk 447 optimal weight: 50.0000 chunk 386 optimal weight: 20.0000 chunk 300 optimal weight: 0.0470 chunk 283 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 317 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 534 GLN 1 804 ASN ** 11002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11107 GLN 2 458 ASN 3 219 HIS 3 363 HIS 3 518 GLN 3 575 ASN C 400 HIS C 445 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.255031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200712 restraints weight = 62415.394| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 5.57 r_work: 0.3295 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32959 Z= 0.163 Angle : 0.614 12.046 44545 Z= 0.316 Chirality : 0.045 0.210 3946 Planarity : 0.005 0.065 5945 Dihedral : 14.680 154.848 7305 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 6.21 % Allowed : 22.55 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 4597 helix: 0.94 (0.13), residues: 1624 sheet: -0.36 (0.16), residues: 995 loop : -1.68 (0.12), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 464 TYR 0.027 0.002 TYR D 209 PHE 0.020 0.002 PHE 11153 TRP 0.009 0.002 TRP 1 732 HIS 0.015 0.002 HIS 11007 Details of bonding type rmsd covalent geometry : bond 0.00374 (32944) covalent geometry : angle 0.60716 (44527) hydrogen bonds : bond 0.04606 ( 1684) hydrogen bonds : angle 4.31091 ( 4730) metal coordination : bond 0.01101 ( 15) metal coordination : angle 4.69498 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 346 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 503 LYS cc_start: 0.5850 (tttp) cc_final: 0.5448 (mmtp) REVERT: 1 558 ARG cc_start: 0.7268 (mmp80) cc_final: 0.6787 (mmp80) REVERT: 1 564 ASP cc_start: 0.7243 (m-30) cc_final: 0.6990 (m-30) REVERT: 1 566 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7111 (mp) REVERT: 1 835 ASP cc_start: 0.7860 (m-30) cc_final: 0.7554 (m-30) REVERT: 1 839 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: 1 890 GLU cc_start: 0.7098 (tt0) cc_final: 0.6631 (tp30) REVERT: 1 926 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6662 (mmmm) REVERT: 1 931 GLN cc_start: 0.7199 (mt0) cc_final: 0.6694 (mp10) REVERT: 1 957 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7437 (mtm-85) REVERT: 1 967 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3597 (tp30) REVERT: 1 971 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6026 (ttm) REVERT: 1 1037 ASP cc_start: 0.8541 (m-30) cc_final: 0.8212 (m-30) REVERT: 1 1135 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: 1 1160 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: 1 1161 MET cc_start: 0.9123 (ttm) cc_final: 0.8870 (ttm) REVERT: 3 114 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8498 (ttp-170) REVERT: 3 151 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7737 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: 3 273 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9161 (mmm160) REVERT: 3 316 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: 3 326 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8575 (mtt180) REVERT: 3 377 MET cc_start: 0.8578 (mtt) cc_final: 0.8159 (mtp) REVERT: 3 573 GLN cc_start: 0.2591 (OUTLIER) cc_final: 0.2365 (mm-40) REVERT: 3 574 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1272 (pt) REVERT: 3 715 MET cc_start: 0.7266 (mmm) cc_final: 0.7011 (mmm) REVERT: 3 749 GLN cc_start: 0.1467 (OUTLIER) cc_final: 0.0982 (mt0) REVERT: 3 809 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: 3 821 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: 3 873 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: 3 1143 HIS cc_start: 0.8778 (m90) cc_final: 0.8077 (t-90) REVERT: 3 1188 ASN cc_start: 0.7789 (p0) cc_final: 0.7501 (p0) REVERT: 6 25 LYS cc_start: 0.8432 (ttpt) cc_final: 0.7432 (pttm) REVERT: 6 54 TYR cc_start: 0.8452 (m-10) cc_final: 0.8201 (m-80) REVERT: C 470 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6255 (ttp80) REVERT: D 143 ASP cc_start: 0.5263 (p0) cc_final: 0.4352 (p0) REVERT: D 147 ASP cc_start: 0.7146 (m-30) cc_final: 0.6927 (m-30) REVERT: D 153 MET cc_start: 0.8584 (mmm) cc_final: 0.8120 (mmp) REVERT: D 189 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8647 (tp) REVERT: D 202 ASP cc_start: 0.7822 (t0) cc_final: 0.7468 (t70) REVERT: D 203 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6828 (mt-10) REVERT: D 204 ASP cc_start: 0.7565 (t70) cc_final: 0.7259 (t70) REVERT: D 242 MET cc_start: 0.6245 (mmm) cc_final: 0.5970 (tmm) REVERT: E 196 LYS cc_start: 0.3932 (OUTLIER) cc_final: 0.3455 (tppt) REVERT: E 205 ASP cc_start: 0.4358 (t0) cc_final: 0.3767 (p0) outliers start: 141 outliers final: 72 residues processed: 458 average time/residue: 0.6757 time to fit residues: 366.8718 Evaluate side-chains 432 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 339 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 566 LEU Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 768 GLU Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 971 MET Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 476 GLU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 873 GLN Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 266 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 380 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 301 optimal weight: 50.0000 chunk 223 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 435 optimal weight: 40.0000 chunk 300 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 550 HIS 1 804 ASN 11107 GLN 11194 HIS 2 458 ASN 2 572 HIS 3 219 HIS 3 363 HIS C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.256395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.199888 restraints weight = 67645.768| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 6.50 r_work: 0.3306 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32959 Z= 0.107 Angle : 0.538 11.852 44545 Z= 0.273 Chirality : 0.041 0.198 3946 Planarity : 0.004 0.062 5945 Dihedral : 14.446 154.869 7300 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 5.50 % Allowed : 23.43 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4597 helix: 1.46 (0.14), residues: 1641 sheet: -0.11 (0.16), residues: 993 loop : -1.49 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 703 TYR 0.016 0.001 TYR D 136 PHE 0.018 0.001 PHE D 168 TRP 0.010 0.001 TRP 1 732 HIS 0.011 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00231 (32944) covalent geometry : angle 0.53364 (44527) hydrogen bonds : bond 0.03516 ( 1684) hydrogen bonds : angle 4.01773 ( 4730) metal coordination : bond 0.00400 ( 15) metal coordination : angle 3.56632 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 365 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7299 (mmp80) cc_final: 0.6805 (mmp80) REVERT: 1 564 ASP cc_start: 0.7267 (m-30) cc_final: 0.7001 (m-30) REVERT: 1 656 LYS cc_start: 0.7276 (mmtm) cc_final: 0.7069 (mmtm) REVERT: 1 835 ASP cc_start: 0.7809 (m-30) cc_final: 0.7523 (m-30) REVERT: 1 839 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: 1 890 GLU cc_start: 0.7070 (tt0) cc_final: 0.6633 (tp30) REVERT: 1 926 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6631 (mmmm) REVERT: 1 931 GLN cc_start: 0.7063 (mt0) cc_final: 0.6596 (mp10) REVERT: 1 946 LYS cc_start: 0.7316 (mppt) cc_final: 0.7105 (tttt) REVERT: 1 957 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7170 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3543 (tp30) REVERT: 1 1037 ASP cc_start: 0.8556 (m-30) cc_final: 0.8219 (m-30) REVERT: 1 1161 MET cc_start: 0.9032 (ttm) cc_final: 0.8751 (ttm) REVERT: 1 1260 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8150 (mttm) REVERT: 2 477 MET cc_start: 0.8873 (tpt) cc_final: 0.8546 (ptm) REVERT: 3 86 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8824 (mtt-85) REVERT: 3 114 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9056 (ttp-170) REVERT: 3 151 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7827 (mtt-85) REVERT: 3 274 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.6317 (mtm180) REVERT: 3 316 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: 3 326 ARG cc_start: 0.9002 (mtt180) cc_final: 0.8585 (mtt180) REVERT: 3 369 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6720 (pp20) REVERT: 3 377 MET cc_start: 0.8466 (mtt) cc_final: 0.8134 (mtp) REVERT: 3 417 ASN cc_start: 0.8354 (t0) cc_final: 0.7868 (m-40) REVERT: 3 469 GLU cc_start: 0.2747 (OUTLIER) cc_final: 0.2489 (tp30) REVERT: 3 574 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1348 (pt) REVERT: 3 630 MET cc_start: 0.3704 (ttm) cc_final: 0.3005 (tpp) REVERT: 3 715 MET cc_start: 0.7258 (mmm) cc_final: 0.7027 (mmm) REVERT: 3 749 GLN cc_start: 0.1432 (OUTLIER) cc_final: 0.0932 (mt0) REVERT: 3 809 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: 3 814 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: 3 821 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: 3 1143 HIS cc_start: 0.8767 (m90) cc_final: 0.8081 (t-90) REVERT: 3 1188 ASN cc_start: 0.7780 (p0) cc_final: 0.7464 (p0) REVERT: 3 1189 LYS cc_start: 0.8424 (mttm) cc_final: 0.8099 (mtmt) REVERT: 6 25 LYS cc_start: 0.8356 (ttpt) cc_final: 0.7332 (pttm) REVERT: 6 54 TYR cc_start: 0.8335 (m-10) cc_final: 0.8087 (m-10) REVERT: C 414 TYR cc_start: 0.7164 (t80) cc_final: 0.6873 (t80) REVERT: C 470 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6382 (ttp80) REVERT: D 131 ARG cc_start: 0.5706 (ttt180) cc_final: 0.5075 (ttt-90) REVERT: D 143 ASP cc_start: 0.5665 (p0) cc_final: 0.4840 (p0) REVERT: D 148 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5927 (pp20) REVERT: D 202 ASP cc_start: 0.7885 (t0) cc_final: 0.7540 (t70) REVERT: D 203 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 204 ASP cc_start: 0.7544 (t70) cc_final: 0.7234 (t70) REVERT: E 169 LYS cc_start: 0.6593 (mttt) cc_final: 0.5753 (ttpt) REVERT: E 196 LYS cc_start: 0.3765 (OUTLIER) cc_final: 0.3467 (tppt) REVERT: E 205 ASP cc_start: 0.4201 (t0) cc_final: 0.3719 (p0) REVERT: E 237 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6195 (tm-30) outliers start: 125 outliers final: 57 residues processed: 462 average time/residue: 0.7137 time to fit residues: 389.0207 Evaluate side-chains 431 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 369 GLU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 469 GLU Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 814 GLN Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 409 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 433 optimal weight: 50.0000 chunk 413 optimal weight: 0.0270 chunk 394 optimal weight: 50.0000 chunk 141 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 58 optimal weight: 0.4980 chunk 243 optimal weight: 50.0000 chunk 108 optimal weight: 0.0870 overall best weight: 1.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 2 458 ASN 3 219 HIS 3 363 HIS C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.254683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.195069 restraints weight = 67063.949| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 6.74 r_work: 0.3086 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32959 Z= 0.122 Angle : 0.554 11.830 44545 Z= 0.281 Chirality : 0.042 0.179 3946 Planarity : 0.004 0.062 5945 Dihedral : 14.309 153.161 7290 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 5.33 % Allowed : 23.65 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4597 helix: 1.73 (0.14), residues: 1640 sheet: 0.01 (0.17), residues: 989 loop : -1.39 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 31013 TYR 0.016 0.002 TYR D 136 PHE 0.018 0.002 PHE D 168 TRP 0.011 0.001 TRP 1 938 HIS 0.008 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00273 (32944) covalent geometry : angle 0.54903 (44527) hydrogen bonds : bond 0.03780 ( 1684) hydrogen bonds : angle 3.96034 ( 4730) metal coordination : bond 0.00541 ( 15) metal coordination : angle 3.87124 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 356 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7085 (mmp80) cc_final: 0.6771 (mmp80) REVERT: 1 564 ASP cc_start: 0.7314 (m-30) cc_final: 0.7069 (m-30) REVERT: 1 656 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6988 (mmtm) REVERT: 1 835 ASP cc_start: 0.7779 (m-30) cc_final: 0.7481 (m-30) REVERT: 1 839 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: 1 890 GLU cc_start: 0.7084 (tt0) cc_final: 0.6608 (tp30) REVERT: 1 926 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6686 (mmmm) REVERT: 1 931 GLN cc_start: 0.7014 (mt0) cc_final: 0.6510 (mp10) REVERT: 1 957 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7195 (mtp-110) REVERT: 1 967 GLU cc_start: 0.3997 (OUTLIER) cc_final: 0.3569 (tp30) REVERT: 1 1037 ASP cc_start: 0.8605 (m-30) cc_final: 0.8247 (m-30) REVERT: 1 1061 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: 1 1161 MET cc_start: 0.8997 (ttm) cc_final: 0.8729 (ttm) REVERT: 2 458 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5188 (t0) REVERT: 2 477 MET cc_start: 0.8871 (tpt) cc_final: 0.8476 (ptm) REVERT: 2 572 HIS cc_start: 0.5185 (OUTLIER) cc_final: 0.4351 (t-90) REVERT: 3 114 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9055 (ttp-170) REVERT: 3 136 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: 3 151 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7853 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: 3 274 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9038 (mtt180) REVERT: 3 316 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: 3 326 ARG cc_start: 0.9048 (mtt180) cc_final: 0.8610 (mtt180) REVERT: 3 377 MET cc_start: 0.8475 (mtt) cc_final: 0.8067 (mtp) REVERT: 3 574 LEU cc_start: 0.2019 (OUTLIER) cc_final: 0.1260 (pt) REVERT: 3 583 MET cc_start: 0.2796 (mtm) cc_final: 0.1364 (pmm) REVERT: 3 645 MET cc_start: 0.0806 (pp-130) cc_final: -0.0058 (mtt) REVERT: 3 715 MET cc_start: 0.7224 (mmm) cc_final: 0.6965 (mmm) REVERT: 3 721 LEU cc_start: 0.7535 (tt) cc_final: 0.7318 (tp) REVERT: 3 749 GLN cc_start: 0.1254 (OUTLIER) cc_final: 0.0779 (mt0) REVERT: 3 770 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4578 (tp) REVERT: 3 809 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: 3 814 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: 3 821 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: 3 1143 HIS cc_start: 0.8764 (m90) cc_final: 0.7980 (t-90) REVERT: 3 1188 ASN cc_start: 0.7783 (p0) cc_final: 0.7477 (p0) REVERT: 3 1189 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7957 (mtmt) REVERT: 6 25 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7255 (pttm) REVERT: 6 48 GLU cc_start: 0.8018 (pp20) cc_final: 0.7735 (pp20) REVERT: 6 54 TYR cc_start: 0.8396 (m-10) cc_final: 0.8134 (m-10) REVERT: C 414 TYR cc_start: 0.7119 (t80) cc_final: 0.6828 (t80) REVERT: D 143 ASP cc_start: 0.5892 (p0) cc_final: 0.5108 (p0) REVERT: D 148 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5959 (pp20) REVERT: D 153 MET cc_start: 0.8639 (mmp) cc_final: 0.8261 (mmp) REVERT: D 202 ASP cc_start: 0.7887 (t0) cc_final: 0.7499 (t70) REVERT: D 203 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7055 (mt-10) REVERT: D 204 ASP cc_start: 0.7432 (t70) cc_final: 0.7129 (t70) REVERT: E 169 LYS cc_start: 0.6414 (mttt) cc_final: 0.5618 (ttpt) REVERT: E 196 LYS cc_start: 0.3715 (OUTLIER) cc_final: 0.3388 (tppt) REVERT: E 205 ASP cc_start: 0.4145 (t0) cc_final: 0.3650 (p0) REVERT: E 237 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6145 (tm-30) outliers start: 121 outliers final: 61 residues processed: 449 average time/residue: 0.6766 time to fit residues: 359.4398 Evaluate side-chains 430 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 347 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1260 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 581 LYS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 814 GLN Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 418 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 422 optimal weight: 40.0000 chunk 184 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN ** 11002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.253490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.201880 restraints weight = 62796.225| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 4.84 r_work: 0.3133 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32959 Z= 0.161 Angle : 0.597 11.680 44545 Z= 0.305 Chirality : 0.044 0.204 3946 Planarity : 0.005 0.065 5945 Dihedral : 14.326 150.312 7289 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 5.68 % Allowed : 23.16 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4597 helix: 1.79 (0.14), residues: 1639 sheet: 0.05 (0.17), residues: 1003 loop : -1.32 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 31013 TYR 0.019 0.002 TYR 3 926 PHE 0.022 0.002 PHE 11153 TRP 0.011 0.002 TRP 1 938 HIS 0.008 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00373 (32944) covalent geometry : angle 0.59079 (44527) hydrogen bonds : bond 0.04310 ( 1684) hydrogen bonds : angle 4.02195 ( 4730) metal coordination : bond 0.00549 ( 15) metal coordination : angle 4.23800 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 355 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.6975 (mmp80) cc_final: 0.6695 (mmp80) REVERT: 1 564 ASP cc_start: 0.7267 (m-30) cc_final: 0.7055 (m-30) REVERT: 1 656 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6876 (mmtm) REVERT: 1 835 ASP cc_start: 0.7973 (m-30) cc_final: 0.7689 (m-30) REVERT: 1 839 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: 1 890 GLU cc_start: 0.7156 (tt0) cc_final: 0.6715 (tp30) REVERT: 1 926 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6846 (mmmm) REVERT: 1 931 GLN cc_start: 0.7115 (mt0) cc_final: 0.6556 (mp10) REVERT: 1 967 GLU cc_start: 0.4305 (OUTLIER) cc_final: 0.3842 (tp30) REVERT: 1 1037 ASP cc_start: 0.8591 (m-30) cc_final: 0.8247 (m-30) REVERT: 1 1061 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: 1 1161 MET cc_start: 0.9049 (ttm) cc_final: 0.8763 (ttm) REVERT: 2 477 MET cc_start: 0.8924 (tpt) cc_final: 0.8542 (ptm) REVERT: 2 572 HIS cc_start: 0.5334 (OUTLIER) cc_final: 0.4536 (t-90) REVERT: 3 114 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8898 (ttp-170) REVERT: 3 136 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: 3 151 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: 3 273 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.9144 (mmm160) REVERT: 3 274 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.9100 (mtt180) REVERT: 3 316 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: 3 326 ARG cc_start: 0.9057 (mtt180) cc_final: 0.8613 (mtt180) REVERT: 3 377 MET cc_start: 0.8526 (mtt) cc_final: 0.8113 (mtp) REVERT: 3 390 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7832 (ptt90) REVERT: 3 546 LYS cc_start: 0.3477 (OUTLIER) cc_final: 0.3215 (mtmm) REVERT: 3 568 MET cc_start: 0.0440 (mmt) cc_final: 0.0106 (mmt) REVERT: 3 574 LEU cc_start: 0.2190 (OUTLIER) cc_final: 0.1582 (pt) REVERT: 3 583 MET cc_start: 0.3151 (mtm) cc_final: 0.1581 (pmm) REVERT: 3 715 MET cc_start: 0.7089 (mmm) cc_final: 0.6887 (mmm) REVERT: 3 809 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: 3 821 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: 3 1143 HIS cc_start: 0.8764 (m90) cc_final: 0.8003 (t-90) REVERT: 3 1188 ASN cc_start: 0.7827 (p0) cc_final: 0.7482 (p0) REVERT: 3 1189 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: 6 54 TYR cc_start: 0.8467 (m-10) cc_final: 0.8168 (m-10) REVERT: C 414 TYR cc_start: 0.7126 (t80) cc_final: 0.6814 (t80) REVERT: D 143 ASP cc_start: 0.5886 (p0) cc_final: 0.5191 (p0) REVERT: D 153 MET cc_start: 0.8644 (mmp) cc_final: 0.8122 (mmm) REVERT: D 191 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7555 (tmt170) REVERT: D 204 ASP cc_start: 0.7412 (t70) cc_final: 0.7126 (t70) REVERT: E 169 LYS cc_start: 0.6650 (mttt) cc_final: 0.5783 (ttpt) REVERT: E 196 LYS cc_start: 0.4104 (OUTLIER) cc_final: 0.3606 (tppt) REVERT: E 205 ASP cc_start: 0.4070 (t0) cc_final: 0.3668 (p0) REVERT: E 237 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6225 (tm-30) outliers start: 129 outliers final: 70 residues processed: 455 average time/residue: 0.6520 time to fit residues: 352.2774 Evaluate side-chains 444 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 353 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 771 LEU Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 869 MET Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 40 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 398 optimal weight: 0.0170 chunk 146 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 456 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 3 219 HIS 3 363 HIS C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.255639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.203305 restraints weight = 54937.624| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 5.16 r_work: 0.3168 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32959 Z= 0.098 Angle : 0.522 10.585 44545 Z= 0.264 Chirality : 0.040 0.194 3946 Planarity : 0.004 0.062 5945 Dihedral : 14.221 151.247 7289 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 4.40 % Allowed : 24.66 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4597 helix: 2.02 (0.14), residues: 1646 sheet: 0.26 (0.17), residues: 991 loop : -1.23 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 502 TYR 0.016 0.001 TYR D 136 PHE 0.017 0.001 PHE D 168 TRP 0.011 0.001 TRP 1 938 HIS 0.007 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00212 (32944) covalent geometry : angle 0.51788 (44527) hydrogen bonds : bond 0.03203 ( 1684) hydrogen bonds : angle 3.79451 ( 4730) metal coordination : bond 0.00470 ( 15) metal coordination : angle 3.24989 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 360 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7079 (mmp80) cc_final: 0.6780 (mmp80) REVERT: 1 564 ASP cc_start: 0.7282 (m-30) cc_final: 0.7025 (m-30) REVERT: 1 835 ASP cc_start: 0.7947 (m-30) cc_final: 0.7690 (m-30) REVERT: 1 839 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: 1 890 GLU cc_start: 0.7170 (tt0) cc_final: 0.6676 (tp30) REVERT: 1 926 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6908 (mmmm) REVERT: 1 931 GLN cc_start: 0.6952 (mt0) cc_final: 0.6452 (mp10) REVERT: 1 967 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.3973 (tp30) REVERT: 1 971 MET cc_start: 0.6153 (ttm) cc_final: 0.5904 (ttm) REVERT: 1 1037 ASP cc_start: 0.8624 (m-30) cc_final: 0.8277 (m-30) REVERT: 1 1061 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: 1 1161 MET cc_start: 0.8947 (ttm) cc_final: 0.8687 (ttm) REVERT: 2 477 MET cc_start: 0.8850 (tpt) cc_final: 0.8534 (ptm) REVERT: 2 572 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4657 (t-90) REVERT: 3 151 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: 3 274 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9007 (mtt180) REVERT: 3 316 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: 3 326 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8555 (mtt180) REVERT: 3 377 MET cc_start: 0.8474 (mtt) cc_final: 0.8094 (mtp) REVERT: 3 390 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7713 (ptt90) REVERT: 3 546 LYS cc_start: 0.3225 (OUTLIER) cc_final: 0.2969 (mtmm) REVERT: 3 574 LEU cc_start: 0.2178 (OUTLIER) cc_final: 0.1611 (pt) REVERT: 3 583 MET cc_start: 0.2978 (mtm) cc_final: 0.1514 (pmm) REVERT: 3 749 GLN cc_start: 0.1878 (OUTLIER) cc_final: 0.1158 (mt0) REVERT: 3 809 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: 3 1143 HIS cc_start: 0.8745 (m90) cc_final: 0.8016 (t-90) REVERT: 3 1188 ASN cc_start: 0.7622 (p0) cc_final: 0.7289 (p0) REVERT: 3 1189 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7995 (mtmt) REVERT: 6 24 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8315 (mm-30) REVERT: 6 25 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7223 (pttm) REVERT: 6 48 GLU cc_start: 0.7994 (pp20) cc_final: 0.7754 (pp20) REVERT: C 414 TYR cc_start: 0.6895 (t80) cc_final: 0.6578 (t80) REVERT: C 465 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7545 (tt0) REVERT: D 143 ASP cc_start: 0.6081 (p0) cc_final: 0.5394 (p0) REVERT: D 148 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.6001 (pp20) REVERT: D 189 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8663 (tp) REVERT: D 191 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7547 (tmt170) REVERT: E 169 LYS cc_start: 0.6528 (mttt) cc_final: 0.5683 (ttpt) REVERT: E 176 LYS cc_start: 0.5385 (tmtt) cc_final: 0.4780 (tmtp) REVERT: E 196 LYS cc_start: 0.3769 (OUTLIER) cc_final: 0.3404 (tppt) REVERT: E 205 ASP cc_start: 0.4031 (t0) cc_final: 0.3618 (p0) REVERT: E 237 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6013 (tm-30) outliers start: 100 outliers final: 53 residues processed: 432 average time/residue: 0.7212 time to fit residues: 367.5996 Evaluate side-chains 420 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 348 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 645 MET Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 420 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 396 optimal weight: 0.2980 chunk 10 optimal weight: 50.0000 chunk 197 optimal weight: 0.7980 chunk 466 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 chunk 292 optimal weight: 0.0470 chunk 222 optimal weight: 8.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN ** 11002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11107 GLN 3 219 HIS 3 363 HIS 3 626 GLN C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.254444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.199942 restraints weight = 71870.711| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 5.72 r_work: 0.3114 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32959 Z= 0.124 Angle : 0.555 11.148 44545 Z= 0.280 Chirality : 0.042 0.225 3946 Planarity : 0.004 0.063 5945 Dihedral : 14.219 149.206 7285 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 4.89 % Allowed : 24.00 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4597 helix: 2.09 (0.14), residues: 1639 sheet: 0.27 (0.17), residues: 1007 loop : -1.17 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 31013 TYR 0.016 0.002 TYR D 136 PHE 0.018 0.002 PHE 11153 TRP 0.016 0.001 TRP 1 938 HIS 0.007 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00282 (32944) covalent geometry : angle 0.55008 (44527) hydrogen bonds : bond 0.03721 ( 1684) hydrogen bonds : angle 3.84508 ( 4730) metal coordination : bond 0.00425 ( 15) metal coordination : angle 3.67538 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 353 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7203 (mmp80) cc_final: 0.6910 (mmp80) REVERT: 1 564 ASP cc_start: 0.7293 (m-30) cc_final: 0.7052 (m-30) REVERT: 1 835 ASP cc_start: 0.7924 (m-30) cc_final: 0.7644 (m-30) REVERT: 1 839 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: 1 890 GLU cc_start: 0.7193 (tt0) cc_final: 0.6699 (tp30) REVERT: 1 926 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6898 (mmmm) REVERT: 1 931 GLN cc_start: 0.6974 (mt0) cc_final: 0.6506 (mp10) REVERT: 1 957 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7409 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.3964 (tp30) REVERT: 1 971 MET cc_start: 0.6081 (ttm) cc_final: 0.5848 (ttm) REVERT: 1 1037 ASP cc_start: 0.8621 (m-30) cc_final: 0.8271 (m-30) REVERT: 1 1061 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: 1 1086 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8179 (tttt) REVERT: 1 1161 MET cc_start: 0.9036 (ttm) cc_final: 0.8752 (ttm) REVERT: 2 477 MET cc_start: 0.8877 (tpt) cc_final: 0.8566 (ptm) REVERT: 2 572 HIS cc_start: 0.5330 (OUTLIER) cc_final: 0.4782 (t-90) REVERT: 3 114 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.9106 (ttp-170) REVERT: 3 151 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7888 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: 3 273 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.9159 (mmm160) REVERT: 3 274 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9053 (mtt180) REVERT: 3 316 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: 3 326 ARG cc_start: 0.9049 (mtt180) cc_final: 0.8597 (mtt180) REVERT: 3 377 MET cc_start: 0.8483 (mtt) cc_final: 0.8082 (mtp) REVERT: 3 390 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7799 (ptt90) REVERT: 3 546 LYS cc_start: 0.3165 (OUTLIER) cc_final: 0.2846 (mtmm) REVERT: 3 574 LEU cc_start: 0.1980 (OUTLIER) cc_final: 0.1517 (pt) REVERT: 3 583 MET cc_start: 0.2994 (mtm) cc_final: 0.1443 (pmm) REVERT: 3 721 LEU cc_start: 0.7556 (tt) cc_final: 0.7216 (tp) REVERT: 3 809 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: 3 1143 HIS cc_start: 0.8784 (m90) cc_final: 0.8024 (t-90) REVERT: 3 1188 ASN cc_start: 0.7600 (p0) cc_final: 0.7263 (p0) REVERT: 3 1189 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8006 (mtmt) REVERT: 6 25 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7263 (pttm) REVERT: 6 48 GLU cc_start: 0.8058 (pp20) cc_final: 0.7822 (pp20) REVERT: 6 54 TYR cc_start: 0.8414 (m-10) cc_final: 0.8151 (m-10) REVERT: C 414 TYR cc_start: 0.6950 (t80) cc_final: 0.6609 (t80) REVERT: C 465 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7452 (tt0) REVERT: D 143 ASP cc_start: 0.5919 (p0) cc_final: 0.5305 (p0) REVERT: D 148 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5993 (pp20) REVERT: D 153 MET cc_start: 0.8581 (mmp) cc_final: 0.8058 (mmm) REVERT: D 189 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8680 (tp) REVERT: D 202 ASP cc_start: 0.7725 (t70) cc_final: 0.7125 (t70) REVERT: D 242 MET cc_start: 0.6708 (mmp) cc_final: 0.6192 (tmm) REVERT: E 169 LYS cc_start: 0.6487 (mttt) cc_final: 0.5662 (ttpt) REVERT: E 176 LYS cc_start: 0.5409 (tmtt) cc_final: 0.4840 (tmtp) REVERT: E 177 LYS cc_start: 0.4778 (tptt) cc_final: 0.3750 (ttpm) REVERT: E 196 LYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3471 (tppt) REVERT: E 205 ASP cc_start: 0.4042 (t0) cc_final: 0.3742 (t0) REVERT: E 237 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6050 (tm-30) outliers start: 111 outliers final: 67 residues processed: 439 average time/residue: 0.6526 time to fit residues: 340.5805 Evaluate side-chains 437 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 349 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 857 LEU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 419 ASP Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 446 optimal weight: 50.0000 chunk 221 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 378 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 461 optimal weight: 50.0000 chunk 363 optimal weight: 40.0000 chunk 460 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 11002 ASN 3 219 HIS 3 363 HIS C 400 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.252715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.194022 restraints weight = 59735.349| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 6.02 r_work: 0.3054 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32959 Z= 0.186 Angle : 0.639 9.494 44545 Z= 0.327 Chirality : 0.046 0.230 3946 Planarity : 0.005 0.069 5945 Dihedral : 14.378 140.259 7285 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 4.67 % Allowed : 24.31 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 4597 helix: 1.88 (0.13), residues: 1649 sheet: 0.17 (0.17), residues: 1013 loop : -1.25 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 3 763 TYR 0.021 0.002 TYR 3 926 PHE 0.019 0.002 PHE 11153 TRP 0.019 0.002 TRP 1 938 HIS 0.007 0.002 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00434 (32944) covalent geometry : angle 0.63225 (44527) hydrogen bonds : bond 0.04758 ( 1684) hydrogen bonds : angle 4.07488 ( 4730) metal coordination : bond 0.00697 ( 15) metal coordination : angle 4.58302 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 349 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7092 (mmp80) cc_final: 0.6822 (mmp80) REVERT: 1 564 ASP cc_start: 0.7355 (m-30) cc_final: 0.7116 (m-30) REVERT: 1 835 ASP cc_start: 0.7935 (m-30) cc_final: 0.7673 (m-30) REVERT: 1 839 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: 1 931 GLN cc_start: 0.7230 (mt0) cc_final: 0.6759 (mp10) REVERT: 1 961 VAL cc_start: 0.8019 (t) cc_final: 0.7786 (p) REVERT: 1 967 GLU cc_start: 0.4596 (OUTLIER) cc_final: 0.3936 (tp30) REVERT: 1 1037 ASP cc_start: 0.8587 (m-30) cc_final: 0.8237 (m-30) REVERT: 1 1061 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: 1 1086 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8219 (tttt) REVERT: 1 1161 MET cc_start: 0.9095 (ttm) cc_final: 0.8819 (ttm) REVERT: 2 477 MET cc_start: 0.8887 (tpt) cc_final: 0.8481 (ptm) REVERT: 2 572 HIS cc_start: 0.5481 (OUTLIER) cc_final: 0.5044 (t-90) REVERT: 3 114 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.9045 (ttp-170) REVERT: 3 151 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7846 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: 3 273 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.9140 (mmm160) REVERT: 3 274 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9136 (mtt180) REVERT: 3 316 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: 3 326 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8622 (mtt180) REVERT: 3 377 MET cc_start: 0.8488 (mtt) cc_final: 0.8059 (mtp) REVERT: 3 390 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7870 (ptt90) REVERT: 3 546 LYS cc_start: 0.2612 (OUTLIER) cc_final: 0.2353 (mtmm) REVERT: 3 574 LEU cc_start: 0.1944 (OUTLIER) cc_final: 0.1532 (pt) REVERT: 3 583 MET cc_start: 0.2802 (mtm) cc_final: 0.1456 (pmm) REVERT: 3 645 MET cc_start: 0.0056 (mmm) cc_final: -0.0773 (pp-130) REVERT: 3 721 LEU cc_start: 0.7548 (tt) cc_final: 0.7155 (tp) REVERT: 3 809 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: 3 817 GLN cc_start: 0.8311 (tp40) cc_final: 0.7777 (tp40) REVERT: 3 1143 HIS cc_start: 0.8795 (m90) cc_final: 0.7964 (t-90) REVERT: 3 1188 ASN cc_start: 0.7681 (p0) cc_final: 0.7326 (p0) REVERT: 3 1189 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8046 (mtmt) REVERT: 6 25 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7266 (pttm) REVERT: 6 48 GLU cc_start: 0.8090 (pp20) cc_final: 0.7848 (pp20) REVERT: 6 54 TYR cc_start: 0.8496 (m-10) cc_final: 0.8250 (m-10) REVERT: C 414 TYR cc_start: 0.7113 (t80) cc_final: 0.6871 (t80) REVERT: D 143 ASP cc_start: 0.5675 (p0) cc_final: 0.5114 (p0) REVERT: D 189 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8686 (tp) REVERT: D 242 MET cc_start: 0.6420 (mmp) cc_final: 0.5960 (tmm) REVERT: E 169 LYS cc_start: 0.6442 (mttt) cc_final: 0.5625 (ttpt) REVERT: E 176 LYS cc_start: 0.5420 (tmtt) cc_final: 0.4825 (tmtp) REVERT: E 177 LYS cc_start: 0.4700 (tptt) cc_final: 0.3672 (ttpm) REVERT: E 196 LYS cc_start: 0.4265 (OUTLIER) cc_final: 0.3605 (tppt) REVERT: E 205 ASP cc_start: 0.4057 (t0) cc_final: 0.3781 (t0) REVERT: E 237 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6054 (tm-30) outliers start: 106 outliers final: 70 residues processed: 433 average time/residue: 0.6936 time to fit residues: 355.7207 Evaluate side-chains 435 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 346 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 419 ASP Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 613 THR Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 869 MET Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 135 optimal weight: 0.9990 chunk 462 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 451 optimal weight: 40.0000 chunk 418 optimal weight: 0.6980 chunk 383 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 450 optimal weight: 50.0000 chunk 413 optimal weight: 0.2980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 3 219 HIS 3 363 HIS D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.252582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.192374 restraints weight = 65585.094| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 6.48 r_work: 0.3046 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32959 Z= 0.187 Angle : 0.632 10.846 44545 Z= 0.324 Chirality : 0.046 0.223 3946 Planarity : 0.005 0.066 5945 Dihedral : 14.381 128.341 7281 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 4.36 % Allowed : 24.48 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4597 helix: 1.86 (0.13), residues: 1653 sheet: 0.14 (0.17), residues: 1011 loop : -1.25 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 957 TYR 0.023 0.002 TYR 3 664 PHE 0.025 0.002 PHE 11153 TRP 0.020 0.002 TRP 1 938 HIS 0.007 0.002 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00438 (32944) covalent geometry : angle 0.62617 (44527) hydrogen bonds : bond 0.04574 ( 1684) hydrogen bonds : angle 4.07307 ( 4730) metal coordination : bond 0.00750 ( 15) metal coordination : angle 4.23301 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 344 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7114 (mmp80) cc_final: 0.6818 (mmp80) REVERT: 1 564 ASP cc_start: 0.7348 (m-30) cc_final: 0.7119 (m-30) REVERT: 1 835 ASP cc_start: 0.7889 (m-30) cc_final: 0.7631 (m-30) REVERT: 1 839 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: 1 931 GLN cc_start: 0.7255 (mt0) cc_final: 0.6756 (mp10) REVERT: 1 961 VAL cc_start: 0.7956 (t) cc_final: 0.7725 (p) REVERT: 1 967 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3877 (tp30) REVERT: 1 1037 ASP cc_start: 0.8612 (m-30) cc_final: 0.8242 (m-30) REVERT: 1 1061 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: 1 1086 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8201 (tttt) REVERT: 1 1161 MET cc_start: 0.9113 (ttm) cc_final: 0.8809 (ttm) REVERT: 2 477 MET cc_start: 0.8851 (tpt) cc_final: 0.8504 (ptm) REVERT: 3 114 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.9022 (ttp-170) REVERT: 3 151 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: 3 273 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.9135 (mmm160) REVERT: 3 274 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.9137 (mtt180) REVERT: 3 326 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8650 (mtt180) REVERT: 3 377 MET cc_start: 0.8482 (mtt) cc_final: 0.8047 (mtp) REVERT: 3 390 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7813 (ptt90) REVERT: 3 574 LEU cc_start: 0.2124 (OUTLIER) cc_final: 0.1649 (pt) REVERT: 3 583 MET cc_start: 0.3329 (mtm) cc_final: 0.2043 (pmm) REVERT: 3 645 MET cc_start: 0.0231 (mmm) cc_final: -0.0690 (pp-130) REVERT: 3 721 LEU cc_start: 0.7533 (tt) cc_final: 0.7160 (tp) REVERT: 3 749 GLN cc_start: 0.1756 (OUTLIER) cc_final: 0.1193 (mt0) REVERT: 3 809 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: 3 817 GLN cc_start: 0.8322 (tp40) cc_final: 0.7742 (tp40) REVERT: 3 821 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: 3 1143 HIS cc_start: 0.8772 (m90) cc_final: 0.7942 (t-90) REVERT: 3 1188 ASN cc_start: 0.7564 (p0) cc_final: 0.7223 (p0) REVERT: 3 1189 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7953 (mtmt) REVERT: 6 25 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7254 (pttm) REVERT: 6 54 TYR cc_start: 0.8465 (m-10) cc_final: 0.8198 (m-10) REVERT: C 414 TYR cc_start: 0.7174 (t80) cc_final: 0.6891 (t80) REVERT: C 438 LEU cc_start: 0.7970 (mp) cc_final: 0.7443 (mt) REVERT: D 143 ASP cc_start: 0.5499 (p0) cc_final: 0.4897 (p0) REVERT: D 189 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8700 (tp) REVERT: D 242 MET cc_start: 0.6609 (mmp) cc_final: 0.6025 (tmm) REVERT: E 196 LYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3371 (mmmt) REVERT: E 205 ASP cc_start: 0.4009 (t0) cc_final: 0.3713 (t0) REVERT: E 237 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6122 (tm-30) outliers start: 99 outliers final: 71 residues processed: 424 average time/residue: 0.7099 time to fit residues: 356.7766 Evaluate side-chains 429 residues out of total 4095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 340 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1020 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 613 THR Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 869 MET Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1189 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 99 optimal weight: 0.9990 chunk 309 optimal weight: 0.0770 chunk 208 optimal weight: 0.7980 chunk 446 optimal weight: 50.0000 chunk 250 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 804 ASN 11209 ASN 3 219 HIS 3 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.254970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207975 restraints weight = 49811.434| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.74 r_work: 0.3312 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32959 Z= 0.101 Angle : 0.539 10.172 44545 Z= 0.271 Chirality : 0.041 0.191 3946 Planarity : 0.004 0.063 5945 Dihedral : 14.220 125.681 7277 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 3.35 % Allowed : 25.80 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 4597 helix: 2.05 (0.14), residues: 1671 sheet: 0.36 (0.17), residues: 995 loop : -1.10 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG 1 957 TYR 0.017 0.001 TYR D 136 PHE 0.016 0.001 PHE D 168 TRP 0.018 0.001 TRP 1 938 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00220 (32944) covalent geometry : angle 0.53499 (44527) hydrogen bonds : bond 0.03232 ( 1684) hydrogen bonds : angle 3.78806 ( 4730) metal coordination : bond 0.00399 ( 15) metal coordination : angle 3.22990 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20294.27 seconds wall clock time: 343 minutes 10.54 seconds (20590.54 seconds total)