Starting phenix.real_space_refine on Sun Jul 5 21:34:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vbz_31886/07_2026/7vbz_31886.cif" } resolution = 2.4 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= 0.003 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18107 2.51 5 N 4963 2.21 5 O 5992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29292 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'970': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "M" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 186 Classifications: {'water': 186} Link IDs: {None: 185} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.830 47.688 108.649 1.00 12.05 S ATOM 3060 SG CYS A 425 46.892 44.703 114.897 1.00 17.80 S ATOM 2738 SG CYS A 385 44.700 43.539 108.827 1.00 12.76 S ATOM 2699 SG CYS A 379 42.663 48.669 112.333 1.00 15.41 S ATOM 3961 SG CYS B 113 37.607 60.417 72.352 1.00 24.67 S ATOM 3980 SG CYS B 116 42.806 58.468 76.409 1.00 24.67 S ATOM 4003 SG CYS B 119 43.717 60.896 70.787 1.00 24.67 S ATOM 4332 SG CYS B 162 41.190 55.014 71.794 1.00 16.11 S ATOM 4030 SG CYS B 123 50.122 63.249 66.134 1.00 17.54 S ATOM 4256 SG CYS B 152 48.292 60.983 60.291 1.00 24.67 S ATOM 4303 SG CYS B 158 46.462 57.740 65.689 1.00 24.67 S ATOM 4282 SG CYS B 155 52.239 57.714 64.187 1.00 24.67 S ATOM 5724 SG CYS C 166 55.193 60.583 56.271 1.00 24.67 S ATOM 4996 SG CYS C 72 55.677 61.620 49.912 1.00 14.05 S ATOM 4990 SG CYS C 71 60.975 60.060 53.300 1.00 24.67 S ATOM 5494 SG CYS C 136 57.631 65.633 54.689 1.00 12.00 S ATOM 14949 SG CYS M 131 41.561 59.622 88.364 1.00 9.07 S ATOM 14928 SG CYS M 128 45.222 54.851 85.645 1.00 10.88 S ATOM 14989 SG CYS M 137 47.361 58.554 90.626 1.00 8.93 S ATOM 15321 SG CYS M 179 44.756 60.089 101.770 1.00 12.59 S ATOM 15675 SG CYS M 226 42.213 62.181 97.027 1.00 10.25 S ATOM 15345 SG CYS M 182 39.849 62.309 102.958 1.00 11.98 S ATOM 15298 SG CYS M 176 39.749 57.199 100.081 1.00 8.78 S ATOM 14546 SG CYS M 78 56.668 55.526 106.090 1.00 12.36 S ATOM 14647 SG CYS M 92 54.797 57.964 108.069 1.00 12.36 S ATOM 14435 SG CYS M 64 50.459 57.489 105.862 1.00 10.46 S ATOM 14521 SG CYS M 75 51.527 55.615 103.164 1.00 9.84 S ATOM 21484 SG CYS O 135 31.762 31.007 117.586 1.00 35.57 S ATOM 21518 SG CYS O 140 30.995 27.793 118.848 1.00 37.91 S ATOM 21798 SG CYS O 176 36.286 32.981 120.165 1.00 34.30 S ATOM 21821 SG CYS O 180 36.464 29.651 121.498 1.00 44.39 S ATOM 27631 SG CYS T 86 29.997 47.962 80.977 1.00 14.18 S ATOM 27809 SG CYS T 111 31.148 51.558 81.659 1.00 14.97 S Time building chain proxies: 5.19, per 1000 atoms: 0.18 Number of scatterers: 29292 At special positions: 0 Unit cell: (126.219, 138.572, 164.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 11 15.00 Mg 1 11.99 O 5992 8.00 N 4963 7.00 C 18107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 31 sheets defined 46.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.571A pdb=" N ARG A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.542A pdb=" N GLU A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.596A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.896A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.535A pdb=" N GLU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 4.387A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.986A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.651A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 209 removed outlier: 5.631A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 70 through 81 removed outlier: 4.068A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.508A pdb=" N SER C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 186 Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'E' and resid 24 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 40 through 48 removed outlier: 3.526A pdb=" N LEU F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 103 through 109 removed outlier: 3.569A pdb=" N LEU G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.642A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 62 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 77 through 98 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 19 through 24 removed outlier: 3.580A pdb=" N ALA I 22 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 24 " --> pdb=" O GLN I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.505A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 4.906A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.620A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 211 through 220 removed outlier: 3.866A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA J 218 " --> pdb=" O LEU J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 315 through 323 Processing helix chain 'J' and resid 334 through 338 Processing helix chain 'J' and resid 344 through 349 removed outlier: 3.808A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 354 Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'J' and resid 358 through 362 Processing helix chain 'J' and resid 365 through 369 removed outlier: 3.790A pdb=" N ASP J 368 " --> pdb=" O GLU J 365 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL J 369 " --> pdb=" O MET J 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 365 through 369' Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.055A pdb=" N GLY L 66 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 74 Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 160 through 165 Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.716A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.647A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 136 Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.910A pdb=" N ASP M 224 " --> pdb=" O GLY M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 245 Processing helix chain 'M' and resid 287 through 293 Processing helix chain 'M' and resid 294 through 299 Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.569A pdb=" N PHE M 333 " --> pdb=" O MET M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 removed outlier: 3.696A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 386 removed outlier: 3.985A pdb=" N LEU M 381 " --> pdb=" O GLY M 378 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG M 382 " --> pdb=" O THR M 379 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER M 383 " --> pdb=" O ASP M 380 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 397 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 458 removed outlier: 3.852A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 3.824A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 528 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.120A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 Processing helix chain 'M' and resid 664 through 673 Processing helix chain 'M' and resid 690 through 695 removed outlier: 3.735A pdb=" N PHE M 694 " --> pdb=" O THR M 690 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR M 695 " --> pdb=" O ILE M 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 690 through 695' Processing helix chain 'M' and resid 698 through 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 19 through 31 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.540A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 70 removed outlier: 3.831A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.640A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.775A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 3.935A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 210 Processing helix chain 'P' and resid 51 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 4.073A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 88 through 92 removed outlier: 3.876A pdb=" N HIS Q 92 " --> pdb=" O PRO Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 126 Processing helix chain 'Q' and resid 132 through 140 removed outlier: 4.041A pdb=" N PHE Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 4.261A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.646A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.787A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 310 through 314 removed outlier: 3.632A pdb=" N VAL Q 314 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 374 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 4.143A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.827A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.593A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 72 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.473A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.446A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 58 removed outlier: 6.714A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 67 through 71 removed outlier: 5.126A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.578A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'J' and resid 226 through 228 removed outlier: 5.967A pdb=" N VAL J 226 " --> pdb=" O TYR J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.131A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.910A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.823A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA M 339 " --> pdb=" O PHE M 546 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU M 548 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE M 341 " --> pdb=" O LEU M 548 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL M 338 " --> pdb=" O SER M 365 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.314A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'N' and resid 37 through 41 removed outlier: 5.621A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.957A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.643A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC8, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.721A pdb=" N ARG Q 96 " --> pdb=" O PRO Q 111 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL Q 98 " --> pdb=" O CYS Q 109 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS Q 109 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD1, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD2, first strand: chain 'T' and resid 30 through 31 removed outlier: 4.441A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'T' and resid 83 through 86 1158 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11794 1.40 - 1.62: 17093 1.62 - 1.84: 273 1.84 - 2.06: 2 2.06 - 2.28: 80 Bond restraints: 29242 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.634 -0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C17 970 Q 501 " pdb=" O16 970 Q 501 " ideal model delta sigma weight residual 1.355 1.580 -0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 29237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 39215 3.52 - 7.03: 342 7.03 - 10.55: 50 10.55 - 14.06: 18 14.06 - 17.58: 9 Bond angle restraints: 39634 Sorted by residual: angle pdb=" N ASN M 74 " pdb=" CA ASN M 74 " pdb=" C ASN M 74 " ideal model delta sigma weight residual 111.36 122.04 -10.68 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N TYR I 28 " pdb=" CA TYR I 28 " pdb=" C TYR I 28 " ideal model delta sigma weight residual 111.36 121.69 -10.33 1.09e+00 8.42e-01 8.97e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 125.32 -17.58 1.95e+00 2.62e-01 8.09e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.24 -14.40 1.91e+00 2.73e-01 5.65e+01 angle pdb=" O ASP Q 193 " pdb=" C ASP Q 193 " pdb=" N ILE Q 194 " ideal model delta sigma weight residual 122.09 129.78 -7.69 1.08e+00 8.57e-01 5.06e+01 ... (remaining 39629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 17025 35.13 - 70.26: 549 70.26 - 105.39: 47 105.39 - 140.52: 6 140.52 - 175.64: 4 Dihedral angle restraints: 17631 sinusoidal: 7402 harmonic: 10229 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 73.24 -175.64 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" C MET M 173 " pdb=" N MET M 173 " pdb=" CA MET M 173 " pdb=" CB MET M 173 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 17628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4047 0.111 - 0.223: 204 0.223 - 0.334: 23 0.334 - 0.446: 8 0.446 - 0.557: 4 Chirality restraints: 4286 Sorted by residual: chirality pdb=" CA MET M 173 " pdb=" N MET M 173 " pdb=" C MET M 173 " pdb=" CB MET M 173 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C23 970 Q 501 " pdb=" C14 970 Q 501 " pdb=" C22 970 Q 501 " pdb=" C24 970 Q 501 " both_signs ideal model delta sigma weight residual False 2.59 2.06 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA ASN M 74 " pdb=" N ASN M 74 " pdb=" C ASN M 74 " pdb=" CB ASN M 74 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 4283 not shown) Planarity restraints: 5096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.374 2.00e-02 2.50e+03 3.41e-01 1.45e+03 pdb=" C18 UQ J 402 " 0.358 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.402 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.004 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.390 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.272 2.00e-02 2.50e+03 2.70e-01 9.09e+02 pdb=" C13 UQ J 402 " -0.225 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " -0.373 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.010 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " 0.060 2.00e-02 2.50e+03 2.55e-01 8.15e+02 pdb=" C11 UQ J 402 " -0.113 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " 0.230 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " -0.436 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " 0.258 2.00e-02 2.50e+03 ... (remaining 5093 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 307 2.51 - 3.10: 21186 3.10 - 3.70: 48153 3.70 - 4.30: 75044 4.30 - 4.90: 116827 Nonbonded interactions: 261517 Sorted by model distance: nonbonded pdb=" NZ LYS M 298 " pdb=" O HOH M 901 " model vdw 1.907 3.120 nonbonded pdb=" OD1 ASP Q 137 " pdb=" OE2 GLU Q 148 " model vdw 1.940 3.040 nonbonded pdb=" NH1 ARG Q 333 " pdb=" O HOH Q 601 " model vdw 2.019 3.120 nonbonded pdb=" OE1 GLU M 83 " pdb=" O HOH M 902 " model vdw 2.033 3.040 nonbonded pdb=" OE2 GLU P 127 " pdb=" NZ LYS P 144 " model vdw 2.036 3.120 ... (remaining 261512 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 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 : 0.012 0.780 29280 Z= 0.651 Angle : 0.997 21.532 39717 Z= 0.527 Chirality : 0.060 0.557 4286 Planarity : 0.010 0.341 5096 Dihedral : 16.834 175.645 11052 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.71 % Favored : 96.00 % Rotamer: Outliers : 2.07 % Allowed : 11.57 % Favored : 86.36 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % 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: -0.05 (0.14), residues: 3502 helix: 0.65 (0.14), residues: 1353 sheet: 0.05 (0.26), residues: 363 loop : -0.51 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 538 TYR 0.020 0.002 TYR J 180 PHE 0.022 0.002 PHE Q 458 TRP 0.016 0.002 TRP M 510 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00915 / 0.44 (29242) covalent geometry : angle 0.92733 / 0.53 (39634) SS BOND : bond 0.00214 / 0.11 ( 1) SS BOND : angle 3.97814 / 2.65 ( 2) hydrogen bonds : bond 0.16339 / 11.29 ( 1158) hydrogen bonds : angle 6.60733 / 4.79 ( 3174) metal coordination : bond 0.15582 / 8.50 ( 35) metal coordination : angle 8.16086 / 5.47 ( 81) Misc. bond : bond 0.56083 / 29.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 577 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.7086 (p) cc_final: 0.6818 (t) REVERT: C 49 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8076 (mmpt) REVERT: E 34 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7260 (mm-30) REVERT: F 57 GLU cc_start: 0.6975 (mp0) cc_final: 0.6750 (mp0) REVERT: G 108 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6761 (mt) REVERT: J 97 MET cc_start: 0.9126 (mtt) cc_final: 0.8910 (mtt) REVERT: J 341 GLN cc_start: 0.7964 (tp40) cc_final: 0.7736 (mp10) REVERT: L 70 GLU cc_start: 0.7664 (tt0) cc_final: 0.7421 (tt0) REVERT: L 78 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8636 (ttp80) REVERT: L 151 LYS cc_start: 0.8372 (mttt) cc_final: 0.8078 (mtpt) REVERT: L 152 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7470 (t) REVERT: M 336 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7436 (t0) REVERT: M 451 ILE cc_start: 0.8209 (mt) cc_final: 0.7963 (mm) REVERT: N 25 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7084 (ttt-90) REVERT: O 162 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7166 (mt-10) REVERT: O 200 ASP cc_start: 0.7806 (m-30) cc_final: 0.7460 (m-30) REVERT: O 236 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5777 (mm-30) REVERT: T 37 LYS cc_start: 0.8452 (mttt) cc_final: 0.8205 (mttp) outliers start: 63 outliers final: 19 residues processed: 619 average time/residue: 0.8388 time to fit residues: 591.3397 Evaluate side-chains 438 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 415 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 355 LYS Chi-restraints excluded: chain M residue 598 ASN Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 336 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN A 456 GLN E 95 ASN F 76 ASN I 25 GLN J 323 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN M 331 GLN M 424 HIS M 540 ASN M 598 ASN M 677 GLN M 688 GLN N 13 GLN N 122 GLN N 123 GLN O 74 HIS P 82 ASN P 236 ASN Q 147 ASN Q 285 ASN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107750 restraints weight = 30231.193| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.09 r_work: 0.3027 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29280 Z= 0.126 Angle : 0.664 22.786 39717 Z= 0.301 Chirality : 0.043 0.146 4286 Planarity : 0.005 0.060 5096 Dihedral : 10.114 178.381 4127 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 2.20 % Allowed : 13.61 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % 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: 0.34 (0.14), residues: 3502 helix: 1.10 (0.14), residues: 1389 sheet: 0.30 (0.27), residues: 342 loop : -0.44 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 52 TYR 0.020 0.001 TYR I 28 PHE 0.018 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.011 0.001 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (29242) covalent geometry : angle 0.56804 / 0.30 (39634) SS BOND : bond 0.00465 / 0.24 ( 1) SS BOND : angle 3.69354 / 2.46 ( 2) hydrogen bonds : bond 0.04695 / 3.20 ( 1158) hydrogen bonds : angle 5.27922 / 3.84 ( 3174) metal coordination : bond 0.01404 / 0.89 ( 35) metal coordination : angle 7.63052 / 5.16 ( 81) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 441 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.7146 (p) cc_final: 0.6824 (t) REVERT: A 36 LYS cc_start: 0.7789 (pmtt) cc_final: 0.7559 (mppt) REVERT: B 52 SER cc_start: 0.8415 (m) cc_final: 0.8052 (p) REVERT: C 49 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8242 (mmpt) REVERT: E 29 LYS cc_start: 0.8588 (mttt) cc_final: 0.8280 (mttp) REVERT: E 34 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8247 (mm-30) REVERT: F 35 ASP cc_start: 0.8229 (m-30) cc_final: 0.8021 (m-30) REVERT: F 57 GLU cc_start: 0.7463 (mp0) cc_final: 0.7125 (mp0) REVERT: F 73 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: J 303 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7520 (tpp-160) REVERT: J 341 GLN cc_start: 0.8165 (tp40) cc_final: 0.7894 (mp10) REVERT: L 152 VAL cc_start: 0.7724 (m) cc_final: 0.7406 (t) REVERT: M 451 ILE cc_start: 0.8499 (mt) cc_final: 0.8281 (mm) REVERT: M 696 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8640 (mtt) REVERT: N 25 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7000 (ttt-90) REVERT: O 162 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7529 (mt-10) REVERT: O 200 ASP cc_start: 0.8035 (m-30) cc_final: 0.7628 (m-30) REVERT: O 236 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5774 (mm-30) REVERT: T 37 LYS cc_start: 0.8448 (mttt) cc_final: 0.8148 (mttp) outliers start: 67 outliers final: 26 residues processed: 481 average time/residue: 0.7853 time to fit residues: 431.4978 Evaluate side-chains 437 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 408 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 230 optimal weight: 0.4980 chunk 196 optimal weight: 0.0050 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 323 HIS M 669 ASN M 677 GLN M 688 GLN Q 149 GLN Q 182 ASN T 123 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106381 restraints weight = 30072.877| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.06 r_work: 0.3003 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29280 Z= 0.124 Angle : 0.635 22.434 39717 Z= 0.287 Chirality : 0.043 0.144 4286 Planarity : 0.004 0.055 5096 Dihedral : 9.024 177.852 4095 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 2.40 % Allowed : 14.10 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3502 helix: 1.36 (0.14), residues: 1365 sheet: 0.27 (0.27), residues: 357 loop : -0.35 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.020 0.002 TYR J 180 PHE 0.019 0.002 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (29242) covalent geometry : angle 0.54320 / 0.29 (39634) SS BOND : bond 0.00538 / 0.28 ( 1) SS BOND : angle 3.27103 / 2.18 ( 2) hydrogen bonds : bond 0.04481 / 3.07 ( 1158) hydrogen bonds : angle 5.03335 / 3.66 ( 3174) metal coordination : bond 0.01448 / 0.75 ( 35) metal coordination : angle 7.28566 / 5.00 ( 81) Misc. bond : bond 0.00159 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 425 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.7118 (p) cc_final: 0.6820 (t) REVERT: B 52 SER cc_start: 0.8452 (m) cc_final: 0.8079 (p) REVERT: C 42 ARG cc_start: 0.6092 (tpt170) cc_final: 0.5620 (tmm160) REVERT: C 49 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8250 (mmpt) REVERT: E 34 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: F 31 GLN cc_start: 0.8424 (tp40) cc_final: 0.8220 (tp40) REVERT: F 35 ASP cc_start: 0.8318 (m-30) cc_final: 0.8087 (m-30) REVERT: G 98 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7100 (tp) REVERT: G 142 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7445 (tp40) REVERT: I 103 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7456 (mmt180) REVERT: J 179 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: J 303 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7526 (tpm170) REVERT: L 152 VAL cc_start: 0.7734 (m) cc_final: 0.7404 (t) REVERT: M 451 ILE cc_start: 0.8570 (mt) cc_final: 0.8345 (mm) REVERT: N 25 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7058 (ttt-90) REVERT: O 162 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7499 (mt-10) REVERT: O 236 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5770 (mm-30) REVERT: Q 258 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8373 (tp) REVERT: T 37 LYS cc_start: 0.8468 (mttt) cc_final: 0.7995 (mttp) outliers start: 73 outliers final: 35 residues processed: 466 average time/residue: 0.7883 time to fit residues: 419.7295 Evaluate side-chains 432 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 392 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 70 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 0.0070 chunk 206 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS F 62 GLN I 29 GLN J 72 HIS J 323 HIS M 499 ASN M 677 GLN M 688 GLN N 13 GLN P 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104583 restraints weight = 29792.188| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.03 r_work: 0.2969 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29280 Z= 0.152 Angle : 0.665 21.430 39717 Z= 0.305 Chirality : 0.044 0.170 4286 Planarity : 0.005 0.059 5096 Dihedral : 9.082 173.801 4092 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.73 % Allowed : 14.00 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3502 helix: 1.34 (0.14), residues: 1361 sheet: 0.22 (0.26), residues: 377 loop : -0.31 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.022 0.002 TYR J 180 PHE 0.020 0.002 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (29242) covalent geometry : angle 0.57979 / 0.30 (39634) SS BOND : bond 0.00524 / 0.28 ( 1) SS BOND : angle 3.52901 / 2.35 ( 2) hydrogen bonds : bond 0.04845 / 3.31 ( 1158) hydrogen bonds : angle 5.11111 / 3.71 ( 3174) metal coordination : bond 0.01312 / 0.68 ( 35) metal coordination : angle 7.20071 / 4.93 ( 81) Misc. bond : bond 0.00698 / 0.37 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 407 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6808 (p) REVERT: A 31 SER cc_start: 0.7184 (p) cc_final: 0.6718 (t) REVERT: A 121 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: B 52 SER cc_start: 0.8452 (m) cc_final: 0.8060 (p) REVERT: C 42 ARG cc_start: 0.6107 (tpt170) cc_final: 0.5679 (tmm160) REVERT: C 49 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8212 (mmpt) REVERT: E 34 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: G 142 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: I 70 MET cc_start: 0.7641 (tmt) cc_final: 0.7340 (tmt) REVERT: J 179 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7840 (mtm-85) REVERT: J 341 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: J 373 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8171 (mtmp) REVERT: K 106 GLN cc_start: 0.8143 (tt0) cc_final: 0.7426 (mp10) REVERT: L 152 VAL cc_start: 0.7740 (m) cc_final: 0.7409 (t) REVERT: M 451 ILE cc_start: 0.8594 (mt) cc_final: 0.8382 (mm) REVERT: N 25 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7034 (ttt-90) REVERT: O 88 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8501 (mtt-85) REVERT: O 129 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8038 (tttt) REVERT: O 162 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7559 (mt-10) REVERT: O 236 GLU cc_start: 0.6549 (mt-10) cc_final: 0.5776 (mm-30) REVERT: Q 258 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8439 (tp) REVERT: T 37 LYS cc_start: 0.8562 (mttt) cc_final: 0.8047 (mttp) outliers start: 83 outliers final: 42 residues processed: 454 average time/residue: 0.7992 time to fit residues: 414.9818 Evaluate side-chains 452 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 400 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 240 optimal weight: 0.4980 chunk 331 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 335 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS F 31 GLN M 677 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100073 restraints weight = 29751.059| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.09 r_work: 0.2908 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 29280 Z= 0.248 Angle : 0.767 19.255 39717 Z= 0.369 Chirality : 0.050 0.160 4286 Planarity : 0.006 0.069 5096 Dihedral : 9.745 178.968 4090 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 3.22 % Allowed : 13.71 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % 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: 0.31 (0.14), residues: 3502 helix: 1.02 (0.14), residues: 1353 sheet: 0.25 (0.26), residues: 371 loop : -0.38 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 83 TYR 0.027 0.003 TYR J 180 PHE 0.024 0.003 PHE O 223 TRP 0.017 0.002 TRP M 510 HIS 0.007 0.002 HIS T 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (29242) covalent geometry : angle 0.69668 / 0.37 (39634) SS BOND : bond 0.00566 / 0.30 ( 1) SS BOND : angle 4.57659 / 3.05 ( 2) hydrogen bonds : bond 0.06214 / 4.27 ( 1158) hydrogen bonds : angle 5.41805 / 3.93 ( 3174) metal coordination : bond 0.01775 / 0.91 ( 35) metal coordination : angle 7.10861 / 4.85 ( 81) Misc. bond : bond 0.00775 / 0.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 408 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6881 (p) REVERT: A 31 SER cc_start: 0.7370 (p) cc_final: 0.6881 (t) REVERT: A 425 CYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 52 SER cc_start: 0.8475 (m) cc_final: 0.8065 (p) REVERT: C 42 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5790 (ttp80) REVERT: C 49 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8250 (mmpt) REVERT: E 34 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: F 31 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8198 (tp40) REVERT: G 142 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: J 179 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7993 (mtm-85) REVERT: J 341 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: J 370 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6850 (tmtt) REVERT: J 373 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8180 (mtmp) REVERT: K 95 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8062 (ttpp) REVERT: K 106 GLN cc_start: 0.8253 (tt0) cc_final: 0.7439 (mp10) REVERT: L 152 VAL cc_start: 0.7740 (m) cc_final: 0.7452 (t) REVERT: N 25 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7105 (ttt-90) REVERT: N 107 LYS cc_start: 0.8103 (pttt) cc_final: 0.7713 (ptmt) REVERT: N 144 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6080 (p90) REVERT: O 64 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: O 88 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8552 (mtt-85) REVERT: O 129 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8013 (tttt) REVERT: O 162 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7773 (mt-10) REVERT: O 236 GLU cc_start: 0.6612 (mt-10) cc_final: 0.5846 (mm-30) REVERT: T 37 LYS cc_start: 0.8563 (mttt) cc_final: 0.8096 (mttp) outliers start: 98 outliers final: 51 residues processed: 466 average time/residue: 0.7893 time to fit residues: 422.2997 Evaluate side-chains 460 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 396 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 271 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 62 GLN J 323 HIS M 331 GLN M 677 GLN M 688 GLN N 13 GLN Q 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104551 restraints weight = 29917.598| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.06 r_work: 0.2979 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29280 Z= 0.130 Angle : 0.648 21.420 39717 Z= 0.296 Chirality : 0.043 0.142 4286 Planarity : 0.005 0.064 5096 Dihedral : 9.184 173.505 4090 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 2.53 % Allowed : 14.73 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.50 (0.14), residues: 3502 helix: 1.28 (0.14), residues: 1359 sheet: 0.16 (0.26), residues: 365 loop : -0.32 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.023 0.001 TYR J 216 PHE 0.019 0.001 PHE Q 458 TRP 0.014 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (29242) covalent geometry : angle 0.56016 / 0.29 (39634) SS BOND : bond 0.00637 / 0.34 ( 1) SS BOND : angle 3.49086 / 2.33 ( 2) hydrogen bonds : bond 0.04542 / 3.11 ( 1158) hydrogen bonds : angle 5.11830 / 3.72 ( 3174) metal coordination : bond 0.01204 / 0.62 ( 35) metal coordination : angle 7.22885 / 4.94 ( 81) Misc. bond : bond 0.00500 / 0.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 418 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6866 (p) REVERT: A 31 SER cc_start: 0.7301 (p) cc_final: 0.6855 (t) REVERT: A 451 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: B 52 SER cc_start: 0.8439 (m) cc_final: 0.8080 (p) REVERT: C 42 ARG cc_start: 0.6166 (tpt170) cc_final: 0.5801 (ttp80) REVERT: C 49 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8183 (mmpt) REVERT: E 34 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: E 69 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7931 (mptm) REVERT: G 105 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.5662 (mmp) REVERT: G 142 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7465 (tp40) REVERT: I 113 LEU cc_start: 0.8305 (mt) cc_final: 0.8073 (mt) REVERT: J 179 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7843 (mtm-85) REVERT: J 370 LYS cc_start: 0.6895 (tmtt) cc_final: 0.6582 (tmtt) REVERT: K 106 GLN cc_start: 0.8167 (tt0) cc_final: 0.7433 (mp10) REVERT: L 152 VAL cc_start: 0.7752 (m) cc_final: 0.7419 (t) REVERT: N 21 ARG cc_start: 0.6684 (mtp-110) cc_final: 0.6109 (ttt-90) REVERT: N 25 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7031 (ttt-90) REVERT: N 144 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6019 (p90) REVERT: O 64 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: O 88 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8490 (mtt-85) REVERT: O 129 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8010 (tttt) REVERT: O 162 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7559 (mt-10) REVERT: O 236 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5836 (mm-30) REVERT: T 37 LYS cc_start: 0.8592 (mttt) cc_final: 0.8081 (mttp) outliers start: 77 outliers final: 39 residues processed: 461 average time/residue: 0.7415 time to fit residues: 392.7356 Evaluate side-chains 451 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 400 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 122 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 31 GLN F 62 GLN M 677 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101962 restraints weight = 29810.834| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.04 r_work: 0.2940 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29280 Z= 0.197 Angle : 0.715 19.593 39717 Z= 0.338 Chirality : 0.047 0.249 4286 Planarity : 0.005 0.065 5096 Dihedral : 9.391 177.603 4090 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.66 % Allowed : 14.99 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.38 (0.14), residues: 3502 helix: 1.13 (0.14), residues: 1357 sheet: 0.13 (0.26), residues: 372 loop : -0.35 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.025 0.002 TYR J 180 PHE 0.021 0.002 PHE Q 458 TRP 0.015 0.002 TRP M 510 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (29242) covalent geometry : angle 0.63887 / 0.34 (39634) SS BOND : bond 0.00549 / 0.29 ( 1) SS BOND : angle 4.09326 / 2.73 ( 2) hydrogen bonds : bond 0.05533 / 3.79 ( 1158) hydrogen bonds : angle 5.26197 / 3.82 ( 3174) metal coordination : bond 0.01546 / 0.79 ( 35) metal coordination : angle 7.13175 / 4.88 ( 81) Misc. bond : bond 0.00349 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 400 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5418 (ptpt) REVERT: A 30 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6901 (p) REVERT: A 31 SER cc_start: 0.7424 (p) cc_final: 0.6969 (t) REVERT: A 451 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: B 52 SER cc_start: 0.8439 (m) cc_final: 0.8074 (p) REVERT: B 68 ARG cc_start: 0.8295 (mtp180) cc_final: 0.7983 (ttm-80) REVERT: C 42 ARG cc_start: 0.6222 (tpt170) cc_final: 0.5864 (ttp80) REVERT: C 49 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8232 (mmpt) REVERT: E 23 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6923 (mmm-85) REVERT: E 34 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: E 69 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7912 (mptm) REVERT: F 26 ARG cc_start: 0.7714 (ptp-110) cc_final: 0.7311 (ptp-170) REVERT: F 73 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: G 142 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: I 113 LEU cc_start: 0.8339 (mt) cc_final: 0.8129 (mt) REVERT: J 179 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7944 (mtm-85) REVERT: J 370 LYS cc_start: 0.6992 (tmtt) cc_final: 0.6692 (tmtt) REVERT: J 373 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8192 (mtmp) REVERT: K 106 GLN cc_start: 0.8209 (tt0) cc_final: 0.7474 (mp10) REVERT: L 152 VAL cc_start: 0.7767 (m) cc_final: 0.7462 (t) REVERT: M 150 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8304 (mtt-85) REVERT: N 21 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6097 (ttt-90) REVERT: N 25 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7029 (ttt-90) REVERT: N 144 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6204 (p90) REVERT: O 64 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: O 88 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8543 (mtt-85) REVERT: O 129 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8011 (tttt) REVERT: O 162 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7638 (mt-10) REVERT: O 236 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5860 (mm-30) REVERT: Q 258 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (tt) REVERT: T 37 LYS cc_start: 0.8573 (mttt) cc_final: 0.8131 (mttp) outliers start: 81 outliers final: 50 residues processed: 450 average time/residue: 0.7929 time to fit residues: 409.1116 Evaluate side-chains 463 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 396 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 332 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 31 GLN M 677 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104499 restraints weight = 29953.566| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.05 r_work: 0.2979 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29280 Z= 0.130 Angle : 0.646 21.507 39717 Z= 0.295 Chirality : 0.043 0.181 4286 Planarity : 0.005 0.064 5096 Dihedral : 9.028 178.770 4090 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.37 % Allowed : 15.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.52 (0.14), residues: 3502 helix: 1.30 (0.14), residues: 1359 sheet: 0.06 (0.26), residues: 373 loop : -0.29 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.022 0.001 TYR J 216 PHE 0.019 0.002 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (29242) covalent geometry : angle 0.55882 / 0.29 (39634) SS BOND : bond 0.00578 / 0.30 ( 1) SS BOND : angle 3.39409 / 2.26 ( 2) hydrogen bonds : bond 0.04509 / 3.08 ( 1158) hydrogen bonds : angle 5.07607 / 3.69 ( 3174) metal coordination : bond 0.01169 / 0.60 ( 35) metal coordination : angle 7.19609 / 4.93 ( 81) Misc. bond : bond 0.00366 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 408 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6880 (p) REVERT: A 31 SER cc_start: 0.7347 (p) cc_final: 0.6910 (t) REVERT: A 451 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: B 52 SER cc_start: 0.8408 (m) cc_final: 0.8048 (p) REVERT: B 68 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7984 (ttm-80) REVERT: C 42 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5858 (ttp80) REVERT: C 49 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8216 (mmpt) REVERT: E 34 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: E 69 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7929 (mptm) REVERT: F 25 GLN cc_start: 0.7902 (tt0) cc_final: 0.7695 (tp-100) REVERT: F 26 ARG cc_start: 0.7654 (ptp-110) cc_final: 0.7278 (ptp-170) REVERT: F 73 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: G 142 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7525 (tp40) REVERT: I 101 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (pp) REVERT: I 103 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7523 (ttm-80) REVERT: J 179 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7871 (mtm-85) REVERT: J 370 LYS cc_start: 0.6818 (tmtt) cc_final: 0.6476 (tmtt) REVERT: K 106 GLN cc_start: 0.8190 (tt0) cc_final: 0.7470 (mp10) REVERT: L 152 VAL cc_start: 0.7761 (m) cc_final: 0.7410 (t) REVERT: M 150 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8237 (mtt-85) REVERT: M 498 GLN cc_start: 0.8254 (tp40) cc_final: 0.7699 (tm-30) REVERT: M 670 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: N 21 ARG cc_start: 0.6680 (mtp-110) cc_final: 0.6150 (ttt-90) REVERT: N 25 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7063 (ttt-90) REVERT: N 144 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6178 (p90) REVERT: O 64 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: O 88 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8510 (mtt-85) REVERT: O 162 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7519 (mt-10) REVERT: O 236 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5860 (mm-30) REVERT: P 50 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7496 (mpt180) REVERT: T 37 LYS cc_start: 0.8616 (mttt) cc_final: 0.8127 (mttp) outliers start: 72 outliers final: 46 residues processed: 447 average time/residue: 0.8177 time to fit residues: 417.7362 Evaluate side-chains 458 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 398 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 219 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 327 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 31 GLN F 62 GLN M 677 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103407 restraints weight = 29925.949| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.07 r_work: 0.2959 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29280 Z= 0.158 Angle : 0.673 20.498 39717 Z= 0.311 Chirality : 0.045 0.185 4286 Planarity : 0.005 0.063 5096 Dihedral : 9.024 179.626 4090 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.43 % Allowed : 15.22 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.48 (0.14), residues: 3502 helix: 1.26 (0.14), residues: 1359 sheet: 0.07 (0.26), residues: 378 loop : -0.30 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 44 TYR 0.023 0.002 TYR J 216 PHE 0.020 0.002 PHE Q 458 TRP 0.013 0.001 TRP M 510 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (29242) covalent geometry : angle 0.59045 / 0.31 (39634) SS BOND : bond 0.00581 / 0.31 ( 1) SS BOND : angle 3.65999 / 2.44 ( 2) hydrogen bonds : bond 0.04915 / 3.37 ( 1158) hydrogen bonds : angle 5.12379 / 3.72 ( 3174) metal coordination : bond 0.01293 / 0.66 ( 35) metal coordination : angle 7.14103 / 4.90 ( 81) Misc. bond : bond 0.00393 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 400 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.5446 (ptpt) REVERT: A 30 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6892 (p) REVERT: A 31 SER cc_start: 0.7364 (p) cc_final: 0.6960 (t) REVERT: A 451 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: B 52 SER cc_start: 0.8419 (m) cc_final: 0.8069 (p) REVERT: C 42 ARG cc_start: 0.6191 (tpt170) cc_final: 0.5889 (ttp80) REVERT: C 49 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8243 (mmpt) REVERT: E 34 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: E 69 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7943 (mptm) REVERT: F 25 GLN cc_start: 0.7916 (tt0) cc_final: 0.7713 (tp-100) REVERT: F 26 ARG cc_start: 0.7698 (ptp-110) cc_final: 0.7314 (ptp-170) REVERT: F 73 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: G 142 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: I 70 MET cc_start: 0.7748 (tmt) cc_final: 0.7197 (tmt) REVERT: I 101 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8676 (pp) REVERT: I 103 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7564 (ttm-80) REVERT: J 179 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7937 (mtm-85) REVERT: J 373 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8219 (mtmp) REVERT: K 106 GLN cc_start: 0.8207 (tt0) cc_final: 0.7476 (mp10) REVERT: L 70 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: L 152 VAL cc_start: 0.7774 (m) cc_final: 0.7425 (t) REVERT: M 150 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8275 (mtt-85) REVERT: M 498 GLN cc_start: 0.8284 (tp40) cc_final: 0.7737 (tm-30) REVERT: M 670 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: N 21 ARG cc_start: 0.6682 (mtp-110) cc_final: 0.6159 (ttt-90) REVERT: N 25 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7084 (ttt-90) REVERT: N 144 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6239 (p90) REVERT: O 64 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: O 88 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8531 (mtt-85) REVERT: O 162 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7577 (mt-10) REVERT: O 236 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5876 (mm-30) REVERT: P 50 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7512 (mpt180) REVERT: T 37 LYS cc_start: 0.8589 (mttt) cc_final: 0.8183 (mttp) outliers start: 74 outliers final: 47 residues processed: 443 average time/residue: 0.8276 time to fit residues: 419.3381 Evaluate side-chains 459 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 172 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 62 GLN M 677 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101532 restraints weight = 29754.357| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.04 r_work: 0.2930 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29280 Z= 0.218 Angle : 0.740 19.150 39717 Z= 0.352 Chirality : 0.048 0.226 4286 Planarity : 0.006 0.065 5096 Dihedral : 9.285 178.192 4090 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.37 % Allowed : 15.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3502 helix: 1.07 (0.14), residues: 1355 sheet: 0.15 (0.26), residues: 369 loop : -0.38 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 64 TYR 0.026 0.002 TYR J 180 PHE 0.022 0.002 PHE Q 458 TRP 0.017 0.002 TRP J 300 HIS 0.008 0.002 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (29242) covalent geometry : angle 0.66705 / 0.35 (39634) SS BOND : bond 0.00547 / 0.29 ( 1) SS BOND : angle 4.25089 / 2.83 ( 2) hydrogen bonds : bond 0.05773 / 3.96 ( 1158) hydrogen bonds : angle 5.30493 / 3.86 ( 3174) metal coordination : bond 0.01664 / 0.84 ( 35) metal coordination : angle 7.11977 / 4.89 ( 81) Misc. bond : bond 0.00477 / 0.25 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 391 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5500 (ptpt) REVERT: A 30 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6880 (p) REVERT: A 31 SER cc_start: 0.7452 (p) cc_final: 0.7019 (t) REVERT: A 451 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: B 52 SER cc_start: 0.8438 (m) cc_final: 0.8082 (p) REVERT: C 42 ARG cc_start: 0.6201 (tpt170) cc_final: 0.5908 (ttp80) REVERT: C 49 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8246 (mmpt) REVERT: E 69 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7938 (mptm) REVERT: F 25 GLN cc_start: 0.7988 (tt0) cc_final: 0.7735 (tp-100) REVERT: F 26 ARG cc_start: 0.7788 (ptp-110) cc_final: 0.7396 (ptp-170) REVERT: F 73 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: G 142 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: I 101 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8720 (pp) REVERT: J 179 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7969 (mtm-85) REVERT: J 370 LYS cc_start: 0.7086 (tmtt) cc_final: 0.6869 (tmtt) REVERT: J 373 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8182 (mtmp) REVERT: K 106 GLN cc_start: 0.8254 (tt0) cc_final: 0.7432 (mp10) REVERT: L 70 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: L 152 VAL cc_start: 0.7780 (m) cc_final: 0.7472 (t) REVERT: M 150 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8323 (mtt-85) REVERT: N 21 ARG cc_start: 0.6690 (mtp-110) cc_final: 0.6136 (ttt-90) REVERT: N 25 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7158 (ttt-90) REVERT: N 144 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6267 (p90) REVERT: O 64 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: O 88 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8558 (mtt-85) REVERT: O 129 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8022 (tttt) REVERT: O 162 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7714 (mt-10) REVERT: O 236 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5904 (mm-30) REVERT: P 50 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7497 (mpt180) REVERT: T 37 LYS cc_start: 0.8642 (mttt) cc_final: 0.8153 (mttp) outliers start: 72 outliers final: 46 residues processed: 432 average time/residue: 0.8310 time to fit residues: 409.8403 Evaluate side-chains 450 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 388 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 206 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 68 optimal weight: 0.0060 chunk 268 optimal weight: 0.2980 chunk 314 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 HIS F 31 GLN F 62 GLN M 677 GLN M 678 GLN M 688 GLN N 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103357 restraints weight = 30072.075| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.06 r_work: 0.2956 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29280 Z= 0.157 Angle : 0.680 20.643 39717 Z= 0.316 Chirality : 0.045 0.193 4286 Planarity : 0.005 0.064 5096 Dihedral : 9.096 179.984 4090 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 15.29 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.42 (0.14), residues: 3502 helix: 1.19 (0.14), residues: 1358 sheet: 0.08 (0.26), residues: 376 loop : -0.33 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 64 TYR 0.024 0.002 TYR J 216 PHE 0.020 0.002 PHE Q 458 TRP 0.016 0.001 TRP J 300 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (29242) covalent geometry : angle 0.59838 / 0.31 (39634) SS BOND : bond 0.00513 / 0.27 ( 1) SS BOND : angle 3.51893 / 2.35 ( 2) hydrogen bonds : bond 0.04958 / 3.40 ( 1158) hydrogen bonds : angle 5.18339 / 3.77 ( 3174) metal coordination : bond 0.01317 / 0.68 ( 35) metal coordination : angle 7.15361 / 4.91 ( 81) Misc. bond : bond 0.00384 / 0.20 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13744.46 seconds wall clock time: 233 minutes 59.44 seconds (14039.44 seconds total)