Starting phenix.real_space_refine on Fri Mar 6 11:23:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyn_32210/03_2026/7vyn_32210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyn_32210/03_2026/7vyn_32210.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/7vyn_32210/03_2026/7vyn_32210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyn_32210/03_2026/7vyn_32210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vyn_32210/03_2026/7vyn_32210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyn_32210/03_2026/7vyn_32210.map" } 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 18109 2.51 5 N 4960 2.21 5 O 5999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29298 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: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "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: "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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'UQ1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 196 Classifications: {'water': 196} Link IDs: {None: 195} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "T" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} 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 47.925 49.106 104.022 1.00 5.90 S ATOM 3060 SG CYS A 425 47.558 45.870 109.827 1.00 9.53 S ATOM 2738 SG CYS A 385 44.872 44.658 104.122 1.00 7.62 S ATOM 2699 SG CYS A 379 42.710 49.551 108.143 1.00 8.84 S ATOM 3961 SG CYS B 113 34.735 64.668 69.716 1.00 5.36 S ATOM 3980 SG CYS B 116 40.119 62.565 73.234 1.00 1.01 S ATOM 4003 SG CYS B 119 40.912 65.347 67.761 1.00 5.44 S ATOM 4332 SG CYS B 162 38.591 59.454 68.442 1.00 0.00 S ATOM 4030 SG CYS B 123 46.721 68.446 63.028 1.00 0.00 S ATOM 4256 SG CYS B 152 44.806 66.769 57.108 1.00 0.00 S ATOM 4303 SG CYS B 158 43.184 62.948 62.215 1.00 8.70 S ATOM 4282 SG CYS B 155 49.082 63.230 60.419 1.00 0.00 S ATOM 5724 SG CYS C 166 51.172 67.151 52.678 1.00 4.06 S ATOM 4996 SG CYS C 72 51.382 68.620 46.306 1.00 0.00 S ATOM 4990 SG CYS C 71 56.824 66.996 49.099 1.00 0.00 S ATOM 5494 SG CYS C 136 53.314 72.164 51.463 1.00 2.66 S ATOM 14949 SG CYS M 131 39.805 62.546 85.322 1.00 0.00 S ATOM 14928 SG CYS M 128 43.480 58.238 82.043 1.00 2.35 S ATOM 14989 SG CYS M 137 45.624 61.867 87.261 1.00 3.51 S ATOM 15321 SG CYS M 179 44.313 61.686 98.508 1.00 3.92 S ATOM 15675 SG CYS M 226 40.856 64.321 94.317 1.00 6.69 S ATOM 15345 SG CYS M 182 38.754 64.118 100.408 1.00 11.02 S ATOM 15298 SG CYS M 176 38.659 58.664 97.018 1.00 5.63 S ATOM 14546 SG CYS M 78 56.148 57.445 101.744 1.00 3.83 S ATOM 14647 SG CYS M 92 54.388 59.571 104.186 1.00 7.69 S ATOM 14435 SG CYS M 64 49.969 59.174 102.206 1.00 8.47 S ATOM 14521 SG CYS M 75 50.962 57.409 99.034 1.00 0.00 S ATOM 21484 SG CYS O 135 32.911 30.938 112.507 1.00 22.88 S ATOM 21518 SG CYS O 140 32.921 27.480 113.716 1.00 28.96 S ATOM 21798 SG CYS O 176 37.288 32.610 114.991 1.00 29.20 S ATOM 21821 SG CYS O 180 37.926 29.422 116.059 1.00 26.97 S ATOM 27631 SG CYS T 86 28.154 51.043 77.738 1.00 19.02 S ATOM 27809 SG CYS T 111 29.305 54.579 78.510 1.00 8.11 S Time building chain proxies: 6.69, per 1000 atoms: 0.23 Number of scatterers: 29298 At special positions: 0 Unit cell: (121.867, 140.531, 160.293, 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 5999 8.00 N 4960 7.00 C 18109 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=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " 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="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " 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="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " 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: 152 helices and 31 sheets defined 45.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.735A pdb=" N GLY A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.661A pdb=" N GLU A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.868A 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 204 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: 3.623A 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 removed outlier: 3.628A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) 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 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: 4.373A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 4.004A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 457 Proline residue: A 434 - end of helix removed outlier: 3.592A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.563A 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: 5.680A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.011A 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 71 through 81 removed outlier: 3.816A 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 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 removed outlier: 3.551A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.524A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.961A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) 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: 3.751A 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 111 through 127 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.677A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 removed outlier: 3.513A pdb=" N LYS H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.771A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 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: 3.596A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 3.515A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.210A 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: 3.672A 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 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 220 through 224 removed outlier: 3.502A pdb=" N PHE J 223 " --> pdb=" O MET J 220 " (cutoff:3.500A) 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 324 Processing helix chain 'J' and resid 335 through 339 Processing helix chain 'J' and resid 344 through 348 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 removed outlier: 3.523A pdb=" N LEU J 362 " --> pdb=" O TYR J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 369 removed outlier: 3.647A pdb=" N ASP J 368 " --> pdb=" O GLU J 365 " (cutoff:3.500A) removed outlier: 4.296A 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 removed outlier: 3.745A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 69 through 74 Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.521A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.843A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.619A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 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: 3.999A pdb=" N ASP M 224 " --> pdb=" O GLY M 220 " (cutoff:3.500A) 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: 3.710A 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: 3.518A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.701A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 394 removed outlier: 3.530A pdb=" N GLY M 393 " --> pdb=" O THR M 389 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 389 through 394' 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 457 removed outlier: 3.920A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 3.546A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 483 removed outlier: 3.518A pdb=" N GLN M 482 " --> pdb=" O SER M 479 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG M 483 " --> pdb=" O ALA M 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 479 through 483' Processing helix chain 'M' and resid 485 through 504 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.044A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 3.554A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG M 655 " --> pdb=" O ASN M 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 655' Processing helix chain 'M' and resid 664 through 673 Processing helix chain 'M' and resid 690 through 694 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: 3.662A 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 68 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 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: 3.627A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.777A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.033A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 210 Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.651A pdb=" N HIS P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 3.962A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG P 168 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 126 Processing helix chain 'Q' and resid 128 through 140 removed outlier: 3.588A pdb=" N LEU Q 133 " --> pdb=" O TYR Q 129 " (cutoff:3.500A) Proline residue: Q 134 - end of helix removed outlier: 3.858A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.593A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 3.757A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 263 removed outlier: 3.638A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.738A 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 372 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 434 removed outlier: 4.018A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 439 Processing helix chain 'Q' and resid 443 through 454 Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.812A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 5.054A pdb=" N LYS A 184 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A 193 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR A 191 " --> pdb=" O ALA A 186 " (cutoff:3.500A) 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 removed outlier: 6.421A pdb=" N LYS B 39 " --> pdb=" O ILE Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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: 6.461A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.756A 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: 6.324A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 161 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 56 removed outlier: 8.561A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 3.558A 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: 5.165A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU P 111 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.624A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.422A 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: 5.937A 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: 9.184A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.870A 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: 7.790A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'M' and resid 366 through 368 removed outlier: 6.818A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.896A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.701A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 169 through 174 Processing sheet with id=AC7, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.864A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC9, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.410A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD2, first strand: chain 'Q' and resid 394 through 402 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 1145 hydrogen bonds defined for protein. 3165 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: 5.68 Time building geometry restraints manager: 3.51 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: 11787 1.40 - 1.62: 17091 1.62 - 1.84: 281 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 29239 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.631 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 29234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 39310 3.33 - 6.65: 233 6.65 - 9.98: 54 9.98 - 13.31: 19 13.31 - 16.63: 11 Bond angle restraints: 39627 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.37 -16.63 1.95e+00 2.62e-01 7.25e+01 angle pdb=" N LEU L 111 " pdb=" CA LEU L 111 " pdb=" C LEU L 111 " ideal model delta sigma weight residual 111.14 119.28 -8.14 1.08e+00 8.57e-01 5.69e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.27 -14.43 1.91e+00 2.73e-01 5.67e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.68 7.78 1.17e+00 7.36e-01 4.45e+01 angle pdb=" C THR O 164 " pdb=" N PRO O 165 " pdb=" CA PRO O 165 " ideal model delta sigma weight residual 119.05 126.40 -7.35 1.11e+00 8.12e-01 4.38e+01 ... (remaining 39622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 16988 34.41 - 68.83: 647 68.83 - 103.24: 68 103.24 - 137.66: 5 137.66 - 172.07: 7 Dihedral angle restraints: 17715 sinusoidal: 7486 harmonic: 10229 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -137.05 51.05 1 1.00e+01 1.00e-02 3.56e+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 180.00 150.17 29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLU M 283 " pdb=" C GLU M 283 " pdb=" N GLU M 284 " pdb=" CA GLU M 284 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 17712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4018 0.095 - 0.190: 253 0.190 - 0.285: 9 0.285 - 0.380: 2 0.380 - 0.475: 1 Chirality restraints: 4283 Sorted by residual: chirality pdb=" CA LYS O 167 " pdb=" N LYS O 167 " pdb=" C LYS O 167 " pdb=" CB LYS O 167 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C6 PLX C 303 " pdb=" C7 PLX C 303 " pdb=" O6 PLX C 303 " pdb=" O7 PLX C 303 " both_signs ideal model delta sigma weight residual False 2.01 2.33 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4280 not shown) Planarity restraints: 5096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 Q 501 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C11 UQ1 Q 501 " -0.011 2.00e-02 2.50e+03 pdb=" C7 UQ1 Q 501 " -0.295 2.00e-02 2.50e+03 pdb=" C8 UQ1 Q 501 " 0.269 2.00e-02 2.50e+03 pdb=" C9 UQ1 Q 501 " 0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " 0.315 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C11 UQ J 402 " 0.016 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " 0.271 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " -0.235 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.218 2.00e-02 2.50e+03 2.38e-01 7.09e+02 pdb=" C13 UQ J 402 " -0.401 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.239 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.119 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.062 2.00e-02 2.50e+03 ... (remaining 5093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2368 2.74 - 3.28: 28922 3.28 - 3.82: 53088 3.82 - 4.36: 67699 4.36 - 4.90: 106198 Nonbonded interactions: 258275 Sorted by model distance: nonbonded pdb=" OG SER J 178 " pdb=" OD1 ASP J 317 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 84 " pdb=" OE1 GLU C 171 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN Q 149 " pdb=" O HOH Q 601 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU Q 401 " pdb=" O HOH Q 602 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU H 106 " pdb=" OG SER I 72 " model vdw 2.207 3.040 ... (remaining 258270 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: 7.390 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.160 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 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 : 0.009 0.485 29276 Z= 0.472 Angle : 0.859 18.906 39710 Z= 0.411 Chirality : 0.047 0.475 4283 Planarity : 0.010 0.283 5096 Dihedral : 17.576 172.073 11136 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.15 % Allowed : 15.16 % Favored : 83.69 % Cbeta Deviations : 0.03 % 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: 0.41 (0.14), residues: 3502 helix: 1.02 (0.14), residues: 1345 sheet: 0.62 (0.26), residues: 378 loop : -0.33 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 96 TYR 0.018 0.002 TYR Q 214 PHE 0.015 0.002 PHE Q 458 TRP 0.015 0.001 TRP N 61 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00811 (29239) covalent geometry : angle 0.80335 (39627) SS BOND : bond 0.00490 ( 1) SS BOND : angle 3.20714 ( 2) hydrogen bonds : bond 0.14396 ( 1145) hydrogen bonds : angle 6.36250 ( 3165) metal coordination : bond 0.00862 ( 35) metal coordination : angle 6.75838 ( 81) Misc. bond : bond 0.48515 ( 1) *********************** 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 456 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 421 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: F 40 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7598 (ptt180) REVERT: H 96 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.6460 (ttm110) REVERT: M 677 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6109 (pt0) REVERT: N 9 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7367 (mtm180) outliers start: 35 outliers final: 21 residues processed: 444 average time/residue: 0.9197 time to fit residues: 462.8725 Evaluate side-chains 426 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 404 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS E 45 ASN F 93 ASN H 41 ASN H 83 GLN J 269 ASN L 109 ASN M 499 ASN M 705 GLN N 52 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097342 restraints weight = 27754.090| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.05 r_work: 0.2810 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29276 Z= 0.205 Angle : 0.737 19.587 39710 Z= 0.355 Chirality : 0.049 0.177 4283 Planarity : 0.006 0.077 5096 Dihedral : 11.283 175.940 4209 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 3.39 % Allowed : 13.05 % Favored : 83.56 % 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: 1.15 (0.14), residues: 1358 sheet: 0.64 (0.26), residues: 372 loop : -0.29 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 83 TYR 0.024 0.002 TYR J 180 PHE 0.017 0.002 PHE J 195 TRP 0.016 0.002 TRP N 61 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00475 (29239) covalent geometry : angle 0.66564 (39627) SS BOND : bond 0.01230 ( 1) SS BOND : angle 5.18408 ( 2) hydrogen bonds : bond 0.06076 ( 1145) hydrogen bonds : angle 5.40410 ( 3165) metal coordination : bond 0.01365 ( 35) metal coordination : angle 7.01255 ( 81) Misc. bond : bond 0.00141 ( 1) *********************** 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 519 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 416 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8390 (mttp) REVERT: A 451 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7216 (mm-40) REVERT: C 191 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8460 (mtm180) REVERT: E 34 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: F 38 GLU cc_start: 0.7838 (tt0) cc_final: 0.7562 (tt0) REVERT: F 40 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7781 (ptt180) REVERT: I 27 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7549 (ptt90) REVERT: J 289 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8721 (mt) REVERT: J 304 LEU cc_start: 0.8729 (tm) cc_final: 0.8509 (tp) REVERT: M 98 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8476 (tttp) REVERT: M 441 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7736 (ttp-170) outliers start: 103 outliers final: 44 residues processed: 468 average time/residue: 0.9365 time to fit residues: 496.1194 Evaluate side-chains 459 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER 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 F residue 37 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 41 ASN H 83 GLN J 269 ASN L 86 ASN M 460 HIS M 663 ASN M 677 GLN M 705 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098668 restraints weight = 27718.275| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.00 r_work: 0.2809 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29276 Z= 0.183 Angle : 0.700 19.308 39710 Z= 0.334 Chirality : 0.047 0.173 4283 Planarity : 0.006 0.077 5096 Dihedral : 10.912 176.141 4198 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.96 % Allowed : 13.35 % Favored : 83.69 % 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: 0.53 (0.14), residues: 3502 helix: 1.20 (0.14), residues: 1358 sheet: 0.58 (0.26), residues: 374 loop : -0.30 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 83 TYR 0.021 0.002 TYR J 180 PHE 0.017 0.002 PHE N 55 TRP 0.016 0.002 TRP N 61 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00420 (29239) covalent geometry : angle 0.62722 (39627) SS BOND : bond 0.01044 ( 1) SS BOND : angle 4.87406 ( 2) hydrogen bonds : bond 0.05765 ( 1145) hydrogen bonds : angle 5.27908 ( 3165) metal coordination : bond 0.01253 ( 35) metal coordination : angle 6.89020 ( 81) Misc. bond : bond 0.00031 ( 1) *********************** 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 505 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 415 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8383 (mttp) REVERT: A 451 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7165 (mm-40) REVERT: B 114 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9195 (pp) REVERT: C 186 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8102 (mtp-110) REVERT: C 191 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8402 (mtm180) REVERT: E 34 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: F 25 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: F 40 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7684 (ptm160) REVERT: I 27 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7545 (ptt90) REVERT: L 131 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8741 (ttmm) REVERT: M 307 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8756 (pp) REVERT: M 441 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7748 (ttp-170) REVERT: M 454 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: M 675 VAL cc_start: 0.6397 (OUTLIER) cc_final: 0.6178 (p) REVERT: O 106 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7968 (mp10) outliers start: 90 outliers final: 42 residues processed: 463 average time/residue: 0.8795 time to fit residues: 463.0632 Evaluate side-chains 459 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 307 ILE Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 454 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 171 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 498 GLN M 663 ASN M 705 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097535 restraints weight = 27444.875| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.01 r_work: 0.2807 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29276 Z= 0.202 Angle : 0.726 19.423 39710 Z= 0.349 Chirality : 0.048 0.179 4283 Planarity : 0.006 0.079 5096 Dihedral : 10.712 176.338 4196 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 3.35 % Allowed : 12.96 % Favored : 83.69 % 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: 0.49 (0.14), residues: 3502 helix: 1.14 (0.14), residues: 1363 sheet: 0.56 (0.27), residues: 352 loop : -0.31 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 83 TYR 0.022 0.002 TYR J 180 PHE 0.018 0.002 PHE N 55 TRP 0.016 0.002 TRP M 422 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00469 (29239) covalent geometry : angle 0.65508 (39627) SS BOND : bond 0.01112 ( 1) SS BOND : angle 5.07159 ( 2) hydrogen bonds : bond 0.06033 ( 1145) hydrogen bonds : angle 5.32965 ( 3165) metal coordination : bond 0.01311 ( 35) metal coordination : angle 6.91810 ( 81) Misc. bond : bond 0.00005 ( 1) *********************** 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 511 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 409 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: A 451 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7181 (mm-40) REVERT: B 114 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9160 (pp) REVERT: C 191 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8405 (mtm180) REVERT: E 34 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: F 25 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: F 40 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7690 (ptm160) REVERT: I 27 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7566 (ptt90) REVERT: J 304 LEU cc_start: 0.8809 (tm) cc_final: 0.8561 (tp) REVERT: L 131 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8725 (ttmm) REVERT: M 98 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8286 (ttpp) REVERT: M 158 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8794 (ptt-90) REVERT: M 307 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8760 (pp) REVERT: M 441 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7805 (ttp-170) REVERT: M 675 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.6226 (p) REVERT: M 678 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: O 106 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8013 (mp10) outliers start: 102 outliers final: 51 residues processed: 463 average time/residue: 0.9047 time to fit residues: 475.6082 Evaluate side-chains 470 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 404 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 307 ILE Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 12 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 290 optimal weight: 0.0570 chunk 53 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 498 GLN M 663 ASN M 705 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.098987 restraints weight = 27532.527| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.02 r_work: 0.2828 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29276 Z= 0.155 Angle : 0.668 19.201 39710 Z= 0.314 Chirality : 0.046 0.168 4283 Planarity : 0.005 0.075 5096 Dihedral : 10.321 179.776 4196 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 2.99 % Allowed : 13.81 % Favored : 83.20 % 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: 0.60 (0.14), residues: 3502 helix: 1.28 (0.14), residues: 1357 sheet: 0.53 (0.26), residues: 369 loop : -0.26 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 52 TYR 0.020 0.002 TYR J 180 PHE 0.016 0.002 PHE N 55 TRP 0.016 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00351 (29239) covalent geometry : angle 0.59039 (39627) SS BOND : bond 0.00936 ( 1) SS BOND : angle 4.65936 ( 2) hydrogen bonds : bond 0.05234 ( 1145) hydrogen bonds : angle 5.16891 ( 3165) metal coordination : bond 0.01156 ( 35) metal coordination : angle 6.92651 ( 81) Misc. bond : bond 0.00007 ( 1) *********************** 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 504 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 413 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7861 (tmm-80) REVERT: A 401 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: A 451 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7148 (mm-40) REVERT: B 114 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9148 (pp) REVERT: C 191 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8460 (mtm180) REVERT: E 15 THR cc_start: 0.2251 (OUTLIER) cc_final: 0.2011 (m) REVERT: F 25 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: F 40 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7661 (ptm160) REVERT: F 94 VAL cc_start: 0.8491 (t) cc_final: 0.8094 (p) REVERT: I 27 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7556 (ptt90) REVERT: J 158 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 304 LEU cc_start: 0.8822 (tm) cc_final: 0.8579 (tp) REVERT: L 69 GLU cc_start: 0.8411 (tt0) cc_final: 0.8179 (tp30) REVERT: L 131 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8668 (ttmm) REVERT: M 98 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8272 (ttpp) REVERT: M 158 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8755 (ptt-90) REVERT: M 307 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8760 (pp) REVERT: M 441 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7767 (ttp-170) REVERT: M 675 VAL cc_start: 0.6422 (OUTLIER) cc_final: 0.6221 (p) REVERT: M 678 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6606 (mp10) REVERT: Q 463 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8658 (mtm110) REVERT: W 5 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7429 (mttt) outliers start: 91 outliers final: 44 residues processed: 460 average time/residue: 0.8978 time to fit residues: 468.7977 Evaluate side-chains 464 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 114 ILE 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 F residue 25 GLN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 307 ILE Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 374 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL 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 141 optimal weight: 9.9990 chunk 264 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 498 GLN M 663 ASN M 705 GLN Q 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098418 restraints weight = 27501.456| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.11 r_work: 0.2814 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29276 Z= 0.154 Angle : 0.668 19.201 39710 Z= 0.314 Chirality : 0.046 0.166 4283 Planarity : 0.005 0.075 5096 Dihedral : 10.084 176.471 4194 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 3.32 % Allowed : 13.55 % Favored : 83.13 % 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: 0.63 (0.14), residues: 3502 helix: 1.32 (0.14), residues: 1356 sheet: 0.55 (0.26), residues: 372 loop : -0.26 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.020 0.002 TYR J 180 PHE 0.016 0.002 PHE N 55 TRP 0.016 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00350 (29239) covalent geometry : angle 0.59010 (39627) SS BOND : bond 0.00964 ( 1) SS BOND : angle 4.61441 ( 2) hydrogen bonds : bond 0.05214 ( 1145) hydrogen bonds : angle 5.13933 ( 3165) metal coordination : bond 0.01079 ( 35) metal coordination : angle 6.92004 ( 81) Misc. bond : bond 0.00008 ( 1) *********************** 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 506 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 405 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7896 (tmm-80) REVERT: A 401 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (mttp) REVERT: A 451 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7188 (mm-40) REVERT: C 191 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8481 (mtm180) REVERT: E 15 THR cc_start: 0.2346 (OUTLIER) cc_final: 0.2074 (m) REVERT: F 25 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: F 94 VAL cc_start: 0.8511 (t) cc_final: 0.8126 (p) REVERT: I 27 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7541 (ptt90) REVERT: J 158 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7807 (mt-10) REVERT: J 304 LEU cc_start: 0.8835 (tm) cc_final: 0.8606 (tp) REVERT: L 69 GLU cc_start: 0.8482 (tt0) cc_final: 0.8216 (tp30) REVERT: L 131 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8690 (ttmm) REVERT: M 98 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8285 (ttpp) REVERT: M 158 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8764 (ptt-90) REVERT: M 307 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8770 (pp) REVERT: M 441 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7790 (ttp-170) REVERT: M 535 GLU cc_start: 0.7910 (tp30) cc_final: 0.7601 (tm-30) REVERT: M 675 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6287 (p) REVERT: M 678 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: O 106 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: Q 312 ASP cc_start: 0.8757 (p0) cc_final: 0.8493 (p0) REVERT: Q 463 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8665 (mtm110) REVERT: W 5 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7401 (mttt) outliers start: 101 outliers final: 55 residues processed: 456 average time/residue: 0.9084 time to fit residues: 470.6199 Evaluate side-chains 475 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 404 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 73 THR 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 F residue 25 GLN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 307 ILE Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 374 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL 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 250 optimal weight: 3.9990 chunk 287 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 83 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 ASN M 498 GLN M 663 ASN M 705 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.101089 restraints weight = 27881.933| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 0.96 r_work: 0.2879 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29276 Z= 0.109 Angle : 0.611 20.731 39710 Z= 0.277 Chirality : 0.043 0.148 4283 Planarity : 0.004 0.068 5096 Dihedral : 9.515 170.319 4194 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 14.83 % Favored : 83.00 % 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: 0.75 (0.14), residues: 3502 helix: 1.46 (0.14), residues: 1368 sheet: 0.46 (0.26), residues: 377 loop : -0.20 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 52 TYR 0.017 0.001 TYR J 180 PHE 0.016 0.001 PHE Q 458 TRP 0.015 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00233 (29239) covalent geometry : angle 0.52262 (39627) SS BOND : bond 0.00775 ( 1) SS BOND : angle 4.10369 ( 2) hydrogen bonds : bond 0.04120 ( 1145) hydrogen bonds : angle 4.89849 ( 3165) metal coordination : bond 0.00853 ( 35) metal coordination : angle 6.99740 ( 81) Misc. bond : bond 0.00017 ( 1) *********************** 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 490 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 424 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7901 (tmm-80) REVERT: A 401 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: A 451 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: C 191 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8454 (mtm180) REVERT: E 15 THR cc_start: 0.2282 (OUTLIER) cc_final: 0.1999 (m) REVERT: F 25 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7041 (mt0) REVERT: F 40 ARG cc_start: 0.7993 (ptt180) cc_final: 0.7580 (ptm160) REVERT: F 94 VAL cc_start: 0.8501 (t) cc_final: 0.8117 (p) REVERT: I 27 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7550 (ptt90) REVERT: J 158 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7748 (mt-10) REVERT: J 304 LEU cc_start: 0.8793 (tm) cc_final: 0.8570 (tp) REVERT: K 74 ARG cc_start: 0.7783 (mpt-90) cc_final: 0.7552 (mmt90) REVERT: L 69 GLU cc_start: 0.8423 (tt0) cc_final: 0.8207 (tp30) REVERT: M 98 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8421 (tttp) REVERT: M 468 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: M 535 GLU cc_start: 0.7855 (tp30) cc_final: 0.7558 (tm-30) REVERT: Q 312 ASP cc_start: 0.8694 (p0) cc_final: 0.8439 (p0) REVERT: Q 463 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8591 (mtm110) REVERT: W 5 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7382 (mttt) outliers start: 66 outliers final: 30 residues processed: 460 average time/residue: 0.8599 time to fit residues: 449.1602 Evaluate side-chains 453 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 413 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 79 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 101 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 189 optimal weight: 0.1980 chunk 150 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 334 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 498 GLN M 663 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101016 restraints weight = 27708.871| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 0.96 r_work: 0.2864 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29276 Z= 0.115 Angle : 0.617 19.941 39710 Z= 0.280 Chirality : 0.043 0.149 4283 Planarity : 0.005 0.068 5096 Dihedral : 9.267 162.459 4192 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.01 % Allowed : 15.36 % Favored : 82.64 % 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: 0.79 (0.14), residues: 3502 helix: 1.53 (0.14), residues: 1364 sheet: 0.41 (0.26), residues: 386 loop : -0.19 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.017 0.001 TYR J 180 PHE 0.015 0.001 PHE Q 458 TRP 0.015 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00250 (29239) covalent geometry : angle 0.53101 (39627) SS BOND : bond 0.00807 ( 1) SS BOND : angle 4.10090 ( 2) hydrogen bonds : bond 0.04256 ( 1145) hydrogen bonds : angle 4.86344 ( 3165) metal coordination : bond 0.00961 ( 35) metal coordination : angle 6.95111 ( 81) Misc. bond : bond 0.00012 ( 1) *********************** 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 477 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 416 time to evaluate : 1.373 Fit side-chains REVERT: A 174 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7892 (tmm-80) REVERT: A 401 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8286 (mttp) REVERT: A 451 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: C 191 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8450 (mtm180) REVERT: E 15 THR cc_start: 0.2443 (OUTLIER) cc_final: 0.2150 (m) REVERT: E 34 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: E 127 ASP cc_start: 0.7690 (m-30) cc_final: 0.7446 (t70) REVERT: F 40 ARG cc_start: 0.7965 (ptt180) cc_final: 0.7642 (ptm160) REVERT: F 94 VAL cc_start: 0.8505 (t) cc_final: 0.8135 (p) REVERT: I 27 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7544 (ptt90) REVERT: J 158 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7733 (mt-10) REVERT: J 304 LEU cc_start: 0.8784 (tm) cc_final: 0.8582 (tp) REVERT: K 74 ARG cc_start: 0.7798 (mpt-90) cc_final: 0.7577 (mmt90) REVERT: L 59 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7872 (tt) REVERT: L 69 GLU cc_start: 0.8415 (tt0) cc_final: 0.8198 (tp30) REVERT: M 98 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8408 (tttp) REVERT: M 468 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: M 535 GLU cc_start: 0.7855 (tp30) cc_final: 0.7564 (tm-30) REVERT: Q 312 ASP cc_start: 0.8710 (p0) cc_final: 0.8469 (p0) REVERT: Q 463 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8650 (mtm110) outliers start: 61 outliers final: 30 residues processed: 447 average time/residue: 0.8982 time to fit residues: 455.8180 Evaluate side-chains 452 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 412 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 317 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 194 optimal weight: 0.0050 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 45 ASN E 95 ASN F 93 ASN H 83 GLN J 269 ASN M 499 ASN M 663 ASN Q 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.098216 restraints weight = 27615.634| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.00 r_work: 0.2806 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29276 Z= 0.200 Angle : 0.721 19.261 39710 Z= 0.344 Chirality : 0.048 0.178 4283 Planarity : 0.006 0.073 5096 Dihedral : 9.703 161.714 4192 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 15.46 % Favored : 82.47 % 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: 0.64 (0.14), residues: 3502 helix: 1.33 (0.14), residues: 1362 sheet: 0.55 (0.26), residues: 371 loop : -0.26 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 78 TYR 0.023 0.002 TYR J 180 PHE 0.017 0.002 PHE M 462 TRP 0.013 0.002 TRP N 61 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00463 (29239) covalent geometry : angle 0.64900 (39627) SS BOND : bond 0.01061 ( 1) SS BOND : angle 4.65307 ( 2) hydrogen bonds : bond 0.05839 ( 1145) hydrogen bonds : angle 5.20211 ( 3165) metal coordination : bond 0.01377 ( 35) metal coordination : angle 6.92164 ( 81) Misc. bond : bond 0.00014 ( 1) *********************** 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 470 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 1.262 Fit side-chains REVERT: A 174 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7883 (tmm-80) REVERT: A 401 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8370 (mttp) REVERT: A 451 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7189 (mm-40) REVERT: E 15 THR cc_start: 0.2712 (OUTLIER) cc_final: 0.2412 (m) REVERT: E 34 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: F 40 ARG cc_start: 0.8007 (ptt180) cc_final: 0.7680 (ptm160) REVERT: F 94 VAL cc_start: 0.8498 (t) cc_final: 0.8124 (p) REVERT: I 27 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7597 (ptt90) REVERT: J 158 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7754 (mt-10) REVERT: J 304 LEU cc_start: 0.8817 (tm) cc_final: 0.8604 (tp) REVERT: L 59 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7744 (tt) REVERT: L 69 GLU cc_start: 0.8434 (tt0) cc_final: 0.8186 (tp30) REVERT: M 98 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8283 (ttpp) REVERT: M 158 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8801 (ptt-90) REVERT: M 468 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: M 535 GLU cc_start: 0.7877 (tp30) cc_final: 0.7616 (tm-30) REVERT: Q 312 ASP cc_start: 0.8770 (p0) cc_final: 0.8513 (p0) REVERT: Q 463 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8733 (mtm110) REVERT: W 5 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7380 (mttt) outliers start: 63 outliers final: 37 residues processed: 441 average time/residue: 0.9533 time to fit residues: 475.2112 Evaluate side-chains 447 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 398 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 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 159 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 260 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 663 ASN M 705 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 = 0.126695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101273 restraints weight = 27609.128| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 0.95 r_work: 0.2872 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29276 Z= 0.111 Angle : 0.619 20.597 39710 Z= 0.281 Chirality : 0.043 0.153 4283 Planarity : 0.004 0.067 5096 Dihedral : 9.133 153.529 4192 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 1.48 % Allowed : 16.15 % Favored : 82.37 % 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: 0.76 (0.14), residues: 3502 helix: 1.51 (0.14), residues: 1359 sheet: 0.42 (0.26), residues: 374 loop : -0.21 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 52 TYR 0.017 0.001 TYR J 180 PHE 0.016 0.001 PHE Q 458 TRP 0.015 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00238 (29239) covalent geometry : angle 0.53066 (39627) SS BOND : bond 0.00750 ( 1) SS BOND : angle 4.11251 ( 2) hydrogen bonds : bond 0.04114 ( 1145) hydrogen bonds : angle 4.89047 ( 3165) metal coordination : bond 0.00877 ( 35) metal coordination : angle 7.02715 ( 81) Misc. bond : bond 0.00012 ( 1) ********************** 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 453 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 408 time to evaluate : 1.137 Fit side-chains REVERT: A 174 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7893 (tmm-80) REVERT: A 401 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8267 (mttp) REVERT: A 451 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: C 191 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8452 (mtm180) REVERT: E 15 THR cc_start: 0.2626 (OUTLIER) cc_final: 0.2351 (m) REVERT: E 127 ASP cc_start: 0.7671 (m-30) cc_final: 0.7425 (t70) REVERT: F 94 VAL cc_start: 0.8509 (t) cc_final: 0.8134 (p) REVERT: I 27 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: I 70 MET cc_start: 0.7815 (tmt) cc_final: 0.7565 (tmt) REVERT: J 158 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7746 (mt-10) REVERT: J 336 GLU cc_start: 0.7885 (pm20) cc_final: 0.7548 (pm20) REVERT: K 74 ARG cc_start: 0.7783 (mpt-90) cc_final: 0.7575 (mmt90) REVERT: L 59 LEU cc_start: 0.8587 (mt) cc_final: 0.7810 (tt) REVERT: L 69 GLU cc_start: 0.8436 (tt0) cc_final: 0.8211 (tp30) REVERT: L 131 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: M 98 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8239 (ttpp) REVERT: M 467 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7293 (tmmt) REVERT: M 468 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: M 535 GLU cc_start: 0.7852 (tp30) cc_final: 0.7591 (tm-30) REVERT: O 106 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8332 (mp-120) REVERT: Q 312 ASP cc_start: 0.8694 (p0) cc_final: 0.8441 (p0) REVERT: Q 463 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8643 (mtm110) outliers start: 45 outliers final: 28 residues processed: 435 average time/residue: 0.9068 time to fit residues: 446.8094 Evaluate side-chains 444 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 405 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 467 LYS Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 123 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 251 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN H 83 GLN J 269 ASN M 498 GLN M 663 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100470 restraints weight = 27776.776| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 0.97 r_work: 0.2865 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29276 Z= 0.125 Angle : 0.634 19.669 39710 Z= 0.291 Chirality : 0.044 0.161 4283 Planarity : 0.005 0.069 5096 Dihedral : 9.084 150.114 4192 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.58 % Allowed : 15.92 % Favored : 82.51 % 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: 0.77 (0.14), residues: 3502 helix: 1.53 (0.14), residues: 1358 sheet: 0.37 (0.26), residues: 386 loop : -0.21 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 52 TYR 0.018 0.001 TYR J 180 PHE 0.015 0.001 PHE Q 458 TRP 0.015 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00276 (29239) covalent geometry : angle 0.55069 (39627) SS BOND : bond 0.00823 ( 1) SS BOND : angle 4.17226 ( 2) hydrogen bonds : bond 0.04469 ( 1145) hydrogen bonds : angle 4.91214 ( 3165) metal coordination : bond 0.00935 ( 35) metal coordination : angle 6.95626 ( 81) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13467.90 seconds wall clock time: 229 minutes 24.44 seconds (13764.44 seconds total)