Starting phenix.real_space_refine on Fri Mar 6 08:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz1_32218/03_2026/7vz1_32218.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 188 5.16 5 C 17732 2.51 5 N 4886 2.21 5 O 5890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 28737 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1408 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} 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: "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: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2351 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} 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: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} 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: "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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "Q" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} 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 2706 SG CYS A 382 47.173 49.580 102.898 1.00 9.11 S ATOM 3048 SG CYS A 425 46.719 45.900 108.411 1.00 17.70 S ATOM 2726 SG CYS A 385 44.018 45.147 102.621 1.00 4.48 S ATOM 2687 SG CYS A 379 42.032 49.832 107.036 1.00 8.97 S ATOM 3945 SG CYS B 113 34.334 67.403 69.404 1.00 1.16 S ATOM 3964 SG CYS B 116 39.630 64.923 72.860 1.00 8.33 S ATOM 3987 SG CYS B 119 40.403 68.074 67.474 1.00 7.32 S ATOM 4316 SG CYS B 162 37.878 62.187 67.873 1.00 3.29 S ATOM 4014 SG CYS B 123 46.201 71.174 62.828 1.00 0.00 S ATOM 4240 SG CYS B 152 44.169 69.887 56.890 1.00 3.13 S ATOM 4287 SG CYS B 158 42.534 65.811 61.763 1.00 10.01 S ATOM 4266 SG CYS B 155 48.426 66.084 59.865 1.00 0.00 S ATOM 5708 SG CYS C 166 50.420 70.351 52.516 1.00 4.04 S ATOM 4980 SG CYS C 72 50.933 72.111 46.191 1.00 3.36 S ATOM 4974 SG CYS C 71 55.957 70.182 48.534 1.00 0.00 S ATOM 5478 SG CYS C 136 52.815 75.067 51.084 1.00 1.91 S ATOM 14526 SG CYS M 131 39.314 64.113 85.005 1.00 5.86 S ATOM 14505 SG CYS M 128 42.926 60.118 81.345 1.00 9.06 S ATOM 14566 SG CYS M 137 45.250 63.132 86.761 1.00 12.83 S ATOM 14898 SG CYS M 179 43.956 62.498 98.074 1.00 9.35 S ATOM 15252 SG CYS M 226 40.571 65.424 94.012 1.00 6.08 S ATOM 14922 SG CYS M 182 38.550 64.954 100.144 1.00 10.52 S ATOM 14875 SG CYS M 176 38.158 59.762 96.350 1.00 10.08 S ATOM 14123 SG CYS M 78 55.648 57.538 100.919 1.00 10.35 S ATOM 14224 SG CYS M 92 53.986 59.609 103.414 1.00 11.78 S ATOM 14012 SG CYS M 64 49.501 59.534 101.465 1.00 1.40 S ATOM 14098 SG CYS M 75 50.426 57.948 98.233 1.00 7.85 S ATOM 21061 SG CYS O 135 31.399 31.481 110.397 1.00 30.57 S ATOM 21095 SG CYS O 140 31.400 27.938 111.316 1.00 35.42 S ATOM 21375 SG CYS O 176 35.970 32.749 112.857 1.00 25.86 S ATOM 21398 SG CYS O 180 36.551 29.559 113.725 1.00 32.49 S ATOM 27156 SG CYS T 86 27.347 53.707 76.743 1.00 19.19 S ATOM 27334 SG CYS T 111 28.596 57.106 77.822 1.00 15.80 S Time building chain proxies: 6.19, per 1000 atoms: 0.22 Number of scatterers: 28737 At special positions: 0 Unit cell: (121.867, 143.276, 158.647, 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 188 16.00 P 11 15.00 Mg 1 11.99 O 5890 8.00 N 4886 7.00 C 17732 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 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="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " 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="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " 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 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 30 sheets defined 45.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 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: 3.661A pdb=" N GLY A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.835A 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 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.578A 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 Processing helix chain 'A' and resid 405 through 420 removed outlier: 4.071A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 Proline residue: A 434 - end of helix 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: 3.534A 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: 6.031A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (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: 3.933A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.929A pdb=" N SER C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.518A pdb=" N MET C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) 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 187 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.740A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.655A 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 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 48 removed outlier: 6.872A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 97 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 111 through 126 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 37 removed outlier: 3.889A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 64 through 73 removed outlier: 3.628A pdb=" N GLN H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 98 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 75 removed outlier: 3.519A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 4.803A 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: 3.786A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 316 through 324 Processing helix chain 'J' and resid 335 through 339 Processing helix chain 'J' and resid 344 through 347 Processing helix chain 'J' and resid 348 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 'K' and resid 76 through 81 removed outlier: 3.619A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.777A 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 'L' and resid 61 through 65 Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 159 through 164 Processing helix chain 'M' and resid 48 through 57 removed outlier: 3.502A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.516A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 136 Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.532A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.005A 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: 3.520A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (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 360 Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.673A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 426 removed outlier: 3.645A pdb=" N ASP M 426 " --> pdb=" O TRP M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 458 removed outlier: 3.858A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 3.948A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA M 469 " --> pdb=" O ILE M 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 556 through 560 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.169A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 4.061A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) removed outlier: 3.753A 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 672 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 17 removed outlier: 3.643A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.711A 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 69 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: 3.701A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.740A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.300A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 51 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 4.057A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.804A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 140 Proline residue: Q 134 - end of helix removed outlier: 4.033A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.686A 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: 4.340A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.541A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.801A 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 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 439 removed outlier: 4.116A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.691A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 removed outlier: 3.502A pdb=" N VAL Q 461 " --> pdb=" O VAL Q 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.882A 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 194 through 199 removed outlier: 6.251A pdb=" N ALA A 154 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 198 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 156 " --> pdb=" O VAL A 198 " (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: 6.292A 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: 6.496A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 68 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 58 removed outlier: 8.557A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.679A 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: 5.030A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.316A 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: 6.612A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.586A 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 236 through 237 Processing sheet with id=AB3, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB4, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.273A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB8, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.731A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.805A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.997A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.661A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.709A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.702A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC7, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.532A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AC9, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD1, first strand: chain 'T' and resid 30 through 31 removed outlier: 4.076A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD3, first strand: chain 'T' and resid 83 through 86 1143 hydrogen bonds defined for protein. 3147 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: 5.66 Time building geometry restraints manager: 3.38 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: 11550 1.40 - 1.63: 16761 1.63 - 1.85: 279 1.85 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 28670 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+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 1.28e+02 bond pdb=" C2B NDP J 401 " pdb=" C3B NDP J 401 " ideal model delta sigma weight residual 1.552 1.236 0.316 3.50e-02 8.16e+02 8.16e+01 ... (remaining 28665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 38553 3.53 - 7.05: 227 7.05 - 10.58: 41 10.58 - 14.10: 12 14.10 - 17.63: 6 Bond angle restraints: 38839 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 107.74 125.37 -17.63 1.95e+00 2.62e-01 8.14e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.12 -14.28 1.91e+00 2.73e-01 5.56e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.50 7.96 1.17e+00 7.36e-01 4.66e+01 angle pdb=" C ARG A 405 " pdb=" N PRO A 406 " pdb=" CA PRO A 406 " ideal model delta sigma weight residual 119.05 126.55 -7.50 1.11e+00 8.12e-01 4.56e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.16 -8.83 1.32e+00 5.72e-01 4.46e+01 ... (remaining 38834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 16631 33.54 - 67.07: 707 67.07 - 100.61: 66 100.61 - 134.14: 5 134.14 - 167.68: 3 Dihedral angle restraints: 17412 sinusoidal: 7349 harmonic: 10063 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 -135.06 49.06 1 1.00e+01 1.00e-02 3.31e+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 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ARG M 655 " pdb=" C ARG M 655 " pdb=" N TYR M 656 " pdb=" CA TYR M 656 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 17409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3757 0.075 - 0.150: 445 0.150 - 0.224: 12 0.224 - 0.299: 3 0.299 - 0.374: 3 Chirality restraints: 4220 Sorted by residual: 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 3.50e+00 chirality pdb=" CA LYS J 370 " pdb=" N LYS J 370 " pdb=" C LYS J 370 " pdb=" CB LYS J 370 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+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 2.31 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4217 not shown) Planarity restraints: 4997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.102 2.00e-02 2.50e+03 2.39e-01 7.12e+02 pdb=" C3N NDP J 401 " 0.407 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.060 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.267 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.111 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C2N NDP J 401 " 0.116 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.117 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.053 2.00e-02 2.50e+03 7.61e-02 5.78e+01 pdb=" C5N NDP J 401 " 0.093 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.094 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.053 2.00e-02 2.50e+03 ... (remaining 4994 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2729 2.74 - 3.28: 28188 3.28 - 3.82: 51891 3.82 - 4.36: 65765 4.36 - 4.90: 104419 Nonbonded interactions: 252992 Sorted by model distance: nonbonded pdb=" O HOH C 412 " pdb=" O HOH C 454 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP M 162 " pdb=" O HOH M 901 " model vdw 2.206 3.040 nonbonded pdb=" O HOH Q 509 " pdb=" O HOH Q 654 " model vdw 2.208 3.040 nonbonded pdb=" ND2 ASN L 109 " pdb=" O LEU L 111 " model vdw 2.214 3.120 nonbonded pdb=" O PRO Q 366 " pdb=" O HOH Q 501 " model vdw 2.219 3.040 ... (remaining 252987 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 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 : 0.008 0.356 28708 Z= 0.379 Angle : 0.897 40.907 38922 Z= 0.419 Chirality : 0.048 0.374 4220 Planarity : 0.007 0.239 4997 Dihedral : 17.599 167.680 10937 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.17 % Allowed : 15.98 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.11 (0.14), residues: 3439 helix: 0.71 (0.14), residues: 1343 sheet: 0.30 (0.26), residues: 382 loop : -0.42 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 138 TYR 0.019 0.002 TYR P 64 PHE 0.016 0.002 PHE M 238 TRP 0.013 0.001 TRP I 104 HIS 0.013 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00778 (28670) covalent geometry : angle 0.79937 (38839) SS BOND : bond 0.00817 ( 1) SS BOND : angle 2.74872 ( 2) hydrogen bonds : bond 0.14869 ( 1143) hydrogen bonds : angle 6.39698 ( 3147) metal coordination : bond 0.06075 ( 36) metal coordination : angle 8.94445 ( 81) Misc. bond : bond 0.23269 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 432 time to evaluate : 1.081 Fit side-chains REVERT: A 29 LYS cc_start: 0.6162 (ttmt) cc_final: 0.5584 (mptm) REVERT: F 35 ASP cc_start: 0.7660 (m-30) cc_final: 0.7417 (m-30) REVERT: F 57 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: H 73 GLN cc_start: 0.8050 (mm110) cc_final: 0.7439 (mt0) REVERT: K 98 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: M 217 GLU cc_start: 0.8559 (pm20) cc_final: 0.8322 (pm20) outliers start: 35 outliers final: 25 residues processed: 459 average time/residue: 0.8110 time to fit residues: 422.2398 Evaluate side-chains 443 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 416 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN C 123 GLN I 110 GLN J 171 ASN J 251 ASN J 356 HIS L 86 ASN M 39 GLN M 453 GLN M 667 GLN N 52 ASN O 41 HIS O 182 ASN P 131 ASN Q 149 GLN Q 234 GLN Q 431 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095795 restraints weight = 29034.611| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.08 r_work: 0.2777 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.447 28708 Z= 0.203 Angle : 0.755 32.100 38922 Z= 0.346 Chirality : 0.047 0.208 4220 Planarity : 0.006 0.069 4997 Dihedral : 10.947 177.234 4128 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 3.54 % Allowed : 14.17 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.29 (0.14), residues: 3439 helix: 0.97 (0.14), residues: 1341 sheet: 0.23 (0.26), residues: 378 loop : -0.37 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 138 TYR 0.020 0.002 TYR P 64 PHE 0.021 0.002 PHE M 238 TRP 0.013 0.002 TRP M 422 HIS 0.010 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00462 (28670) covalent geometry : angle 0.65007 (38839) SS BOND : bond 0.01174 ( 1) SS BOND : angle 3.63168 ( 2) hydrogen bonds : bond 0.05924 ( 1143) hydrogen bonds : angle 5.27778 ( 3147) metal coordination : bond 0.07618 ( 36) metal coordination : angle 8.41348 ( 81) Misc. bond : bond 0.00238 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 421 time to evaluate : 1.175 Fit side-chains REVERT: A 29 LYS cc_start: 0.6139 (ttmt) cc_final: 0.5397 (mptm) REVERT: A 232 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: A 301 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 47 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7904 (t) REVERT: E 37 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8131 (mtp180) REVERT: F 19 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8655 (pp) REVERT: F 35 ASP cc_start: 0.8186 (m-30) cc_final: 0.7717 (m-30) REVERT: F 57 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: G 123 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6875 (mt-10) REVERT: H 73 GLN cc_start: 0.8112 (mm110) cc_final: 0.7532 (mt0) REVERT: H 95 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8406 (tp) REVERT: I 6 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6759 (ttp-170) REVERT: L 86 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.9059 (t0) REVERT: M 459 ASN cc_start: 0.7754 (m-40) cc_final: 0.7547 (m-40) REVERT: M 643 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.7210 (mtt-85) REVERT: O 50 ASP cc_start: 0.8301 (m-30) cc_final: 0.8089 (m-30) REVERT: Q 197 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6657 (ppp) REVERT: T 105 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6153 (mp0) outliers start: 106 outliers final: 44 residues processed: 480 average time/residue: 0.8352 time to fit residues: 456.0905 Evaluate side-chains 467 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 411 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 129 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 321 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN M 39 GLN M 453 GLN M 499 ASN Q 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097130 restraints weight = 28859.211| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.13 r_work: 0.2802 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 28708 Z= 0.147 Angle : 0.692 38.080 38922 Z= 0.302 Chirality : 0.044 0.197 4220 Planarity : 0.005 0.065 4997 Dihedral : 10.077 146.550 4112 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 2.57 % Allowed : 15.47 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.41 (0.14), residues: 3439 helix: 1.16 (0.14), residues: 1331 sheet: 0.21 (0.26), residues: 385 loop : -0.35 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 138 TYR 0.018 0.001 TYR P 64 PHE 0.015 0.001 PHE N 55 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00322 (28670) covalent geometry : angle 0.56350 (38839) SS BOND : bond 0.00913 ( 1) SS BOND : angle 3.15539 ( 2) hydrogen bonds : bond 0.05070 ( 1143) hydrogen bonds : angle 5.03322 ( 3147) metal coordination : bond 0.05586 ( 36) metal coordination : angle 8.80370 ( 81) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 423 time to evaluate : 1.204 Fit side-chains REVERT: A 29 LYS cc_start: 0.6176 (ttmt) cc_final: 0.5402 (mptm) REVERT: A 301 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: B 47 SER cc_start: 0.8090 (m) cc_final: 0.7867 (t) REVERT: C 99 GLN cc_start: 0.8307 (pt0) cc_final: 0.8041 (mt0) REVERT: E 51 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8043 (mp-120) REVERT: F 19 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8653 (pp) REVERT: F 35 ASP cc_start: 0.8163 (m-30) cc_final: 0.7697 (m-30) REVERT: F 57 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: H 73 GLN cc_start: 0.8075 (mm110) cc_final: 0.7521 (mt0) REVERT: H 95 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8350 (tp) REVERT: I 70 MET cc_start: 0.8075 (tmt) cc_final: 0.7830 (tmt) REVERT: M 459 ASN cc_start: 0.7766 (m-40) cc_final: 0.7560 (m-40) REVERT: O 50 ASP cc_start: 0.8287 (m-30) cc_final: 0.8043 (m-30) REVERT: O 64 GLU cc_start: 0.8232 (tt0) cc_final: 0.7860 (tt0) REVERT: T 105 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6235 (mp0) outliers start: 77 outliers final: 43 residues processed: 467 average time/residue: 0.8253 time to fit residues: 438.5375 Evaluate side-chains 459 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 156 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN E 99 GLN L 86 ASN M 39 GLN M 453 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.095796 restraints weight = 28729.263| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.11 r_work: 0.2776 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.401 28708 Z= 0.174 Angle : 0.709 34.425 38922 Z= 0.317 Chirality : 0.045 0.205 4220 Planarity : 0.005 0.067 4997 Dihedral : 9.524 130.170 4108 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.38 % Allowed : 14.91 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.40 (0.14), residues: 3439 helix: 1.13 (0.14), residues: 1341 sheet: 0.11 (0.26), residues: 380 loop : -0.32 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 138 TYR 0.019 0.002 TYR P 64 PHE 0.017 0.002 PHE N 55 TRP 0.013 0.002 TRP M 422 HIS 0.007 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00390 (28670) covalent geometry : angle 0.59307 (38839) SS BOND : bond 0.01065 ( 1) SS BOND : angle 3.30971 ( 2) hydrogen bonds : bond 0.05430 ( 1143) hydrogen bonds : angle 5.03125 ( 3147) metal coordination : bond 0.06820 ( 36) metal coordination : angle 8.50238 ( 81) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 422 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6236 (ttmt) cc_final: 0.5424 (mptm) REVERT: A 301 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: A 401 LYS cc_start: 0.8075 (mttt) cc_final: 0.7770 (mtmt) REVERT: B 47 SER cc_start: 0.8025 (m) cc_final: 0.7825 (t) REVERT: B 114 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9259 (pp) REVERT: C 99 GLN cc_start: 0.8308 (pt0) cc_final: 0.8060 (mt0) REVERT: E 51 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8073 (mp-120) REVERT: F 19 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8657 (pp) REVERT: F 35 ASP cc_start: 0.8159 (m-30) cc_final: 0.7700 (m-30) REVERT: F 57 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: H 73 GLN cc_start: 0.8075 (mm110) cc_final: 0.7555 (mt0) REVERT: H 95 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8356 (tp) REVERT: I 29 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7579 (mm110) REVERT: J 190 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7963 (mm-30) REVERT: K 102 SER cc_start: 0.8967 (t) cc_final: 0.8745 (m) REVERT: L 156 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: M 215 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6615 (tpt) REVERT: M 643 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: O 50 ASP cc_start: 0.8315 (m-30) cc_final: 0.8072 (m-30) REVERT: O 64 GLU cc_start: 0.8278 (tt0) cc_final: 0.7960 (tt0) REVERT: Q 104 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: T 105 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6305 (mp0) outliers start: 101 outliers final: 54 residues processed: 481 average time/residue: 0.8044 time to fit residues: 439.8651 Evaluate side-chains 471 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 100 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 304 optimal weight: 0.1980 chunk 144 optimal weight: 0.0050 chunk 200 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN L 86 ASN M 39 GLN M 459 ASN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096716 restraints weight = 28798.087| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.22 r_work: 0.2799 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.328 28708 Z= 0.145 Angle : 0.684 37.554 38922 Z= 0.298 Chirality : 0.044 0.199 4220 Planarity : 0.005 0.065 4997 Dihedral : 9.259 145.007 4108 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 3.07 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.46 (0.14), residues: 3439 helix: 1.22 (0.14), residues: 1335 sheet: 0.10 (0.26), residues: 383 loop : -0.31 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 286 TYR 0.018 0.001 TYR P 64 PHE 0.015 0.001 PHE N 55 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00320 (28670) covalent geometry : angle 0.55527 (38839) SS BOND : bond 0.00938 ( 1) SS BOND : angle 3.10637 ( 2) hydrogen bonds : bond 0.04890 ( 1143) hydrogen bonds : angle 4.92495 ( 3147) metal coordination : bond 0.05594 ( 36) metal coordination : angle 8.75149 ( 81) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 421 time to evaluate : 1.159 Fit side-chains REVERT: A 29 LYS cc_start: 0.6275 (tttt) cc_final: 0.5445 (mptm) REVERT: A 301 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: A 401 LYS cc_start: 0.7948 (mttt) cc_final: 0.7620 (mtmt) REVERT: B 114 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9221 (pp) REVERT: C 99 GLN cc_start: 0.8360 (pt0) cc_final: 0.8121 (mt0) REVERT: E 37 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8224 (mtp180) REVERT: E 51 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8077 (mp-120) REVERT: F 19 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (pp) REVERT: F 35 ASP cc_start: 0.8175 (m-30) cc_final: 0.7713 (m-30) REVERT: F 57 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: H 73 GLN cc_start: 0.8047 (mm110) cc_final: 0.7537 (mt0) REVERT: H 95 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8341 (tp) REVERT: I 29 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7538 (mm110) REVERT: J 214 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8658 (mp) REVERT: J 322 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8705 (t) REVERT: K 102 SER cc_start: 0.8979 (t) cc_final: 0.8751 (m) REVERT: L 86 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.9075 (t0) REVERT: L 156 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: M 215 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6340 (tpt) REVERT: M 382 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7698 (mtt180) REVERT: M 643 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.7210 (mtt-85) REVERT: N 8 ARG cc_start: 0.7659 (mmt90) cc_final: 0.7244 (mtt-85) REVERT: O 50 ASP cc_start: 0.8299 (m-30) cc_final: 0.8020 (m-30) REVERT: O 64 GLU cc_start: 0.8299 (tt0) cc_final: 0.8013 (tt0) REVERT: T 105 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6384 (mp0) outliers start: 92 outliers final: 48 residues processed: 478 average time/residue: 0.8109 time to fit residues: 440.1221 Evaluate side-chains 470 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 406 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 11 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 293 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN F 62 GLN H 50 GLN L 86 ASN L 109 ASN M 39 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.096451 restraints weight = 28713.163| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.17 r_work: 0.2770 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.358 28708 Z= 0.156 Angle : 0.689 35.772 38922 Z= 0.304 Chirality : 0.044 0.202 4220 Planarity : 0.005 0.064 4997 Dihedral : 9.211 149.659 4106 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.07 % Allowed : 15.57 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.46 (0.14), residues: 3439 helix: 1.22 (0.14), residues: 1334 sheet: 0.07 (0.25), residues: 383 loop : -0.31 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 138 TYR 0.018 0.002 TYR P 64 PHE 0.015 0.002 PHE J 207 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00345 (28670) covalent geometry : angle 0.56771 (38839) SS BOND : bond 0.00997 ( 1) SS BOND : angle 3.12218 ( 2) hydrogen bonds : bond 0.05041 ( 1143) hydrogen bonds : angle 4.91436 ( 3147) metal coordination : bond 0.06096 ( 36) metal coordination : angle 8.57306 ( 81) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 412 time to evaluate : 1.050 Fit side-chains REVERT: A 29 LYS cc_start: 0.6312 (tttt) cc_final: 0.5467 (mptm) REVERT: A 37 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (t0) REVERT: A 301 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: A 401 LYS cc_start: 0.7950 (mttt) cc_final: 0.7606 (mtmt) REVERT: B 114 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9244 (pp) REVERT: C 65 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: C 99 GLN cc_start: 0.8361 (pt0) cc_final: 0.8121 (mt0) REVERT: E 37 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8226 (mtp180) REVERT: E 51 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8096 (mp-120) REVERT: E 100 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8043 (ttt-90) REVERT: F 19 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8679 (pp) REVERT: F 35 ASP cc_start: 0.8183 (m-30) cc_final: 0.7696 (m-30) REVERT: F 57 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: H 73 GLN cc_start: 0.8054 (mm110) cc_final: 0.7537 (mt0) REVERT: H 95 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8334 (tp) REVERT: J 214 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8654 (mp) REVERT: J 322 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8715 (t) REVERT: K 102 SER cc_start: 0.9007 (t) cc_final: 0.8771 (m) REVERT: L 156 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: M 215 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6348 (tpt) REVERT: M 643 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.7227 (mtt-85) REVERT: M 676 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.6256 (t0) REVERT: N 8 ARG cc_start: 0.7659 (mmt90) cc_final: 0.7246 (mtt-85) REVERT: O 50 ASP cc_start: 0.8315 (m-30) cc_final: 0.8036 (m-30) REVERT: O 64 GLU cc_start: 0.8312 (tt0) cc_final: 0.8032 (tt0) REVERT: Q 104 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: T 105 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6409 (mp0) outliers start: 92 outliers final: 54 residues processed: 471 average time/residue: 0.8169 time to fit residues: 436.6632 Evaluate side-chains 476 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 676 ASN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 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 42 ASN B 59 GLN I 25 GLN M 39 GLN M 453 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.098323 restraints weight = 28756.982| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.20 r_work: 0.2799 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.267 28708 Z= 0.123 Angle : 0.669 39.483 38922 Z= 0.283 Chirality : 0.043 0.190 4220 Planarity : 0.004 0.063 4997 Dihedral : 8.952 157.656 4106 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 2.57 % Allowed : 16.24 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3439 helix: 1.35 (0.14), residues: 1329 sheet: 0.01 (0.26), residues: 384 loop : -0.27 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 23 TYR 0.017 0.001 TYR P 64 PHE 0.014 0.001 PHE B 175 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00266 (28670) covalent geometry : angle 0.53008 (38839) SS BOND : bond 0.00822 ( 1) SS BOND : angle 2.89329 ( 2) hydrogen bonds : bond 0.04422 ( 1143) hydrogen bonds : angle 4.78687 ( 3147) metal coordination : bond 0.04570 ( 36) metal coordination : angle 8.95034 ( 81) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 415 time to evaluate : 1.119 Fit side-chains REVERT: A 29 LYS cc_start: 0.6289 (tttt) cc_final: 0.5391 (mptm) REVERT: A 301 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: A 401 LYS cc_start: 0.7838 (mttt) cc_final: 0.7589 (mtmt) REVERT: B 114 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9209 (pp) REVERT: C 99 GLN cc_start: 0.8381 (pt0) cc_final: 0.8134 (mt0) REVERT: E 51 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8070 (mp-120) REVERT: E 100 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8018 (ttt-90) REVERT: F 19 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8698 (pp) REVERT: F 35 ASP cc_start: 0.8162 (m-30) cc_final: 0.7686 (m-30) REVERT: F 57 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: G 111 ASP cc_start: 0.7247 (p0) cc_final: 0.6871 (p0) REVERT: G 129 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: H 73 GLN cc_start: 0.8060 (mm110) cc_final: 0.7579 (mt0) REVERT: H 95 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8330 (tp) REVERT: J 214 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8651 (mp) REVERT: J 322 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8718 (t) REVERT: K 102 SER cc_start: 0.8994 (t) cc_final: 0.8755 (m) REVERT: L 156 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8165 (mttp) REVERT: M 215 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6355 (tpt) REVERT: M 643 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.7153 (mtt-85) REVERT: M 676 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6204 (t0) REVERT: N 8 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7211 (mtt-85) REVERT: O 50 ASP cc_start: 0.8299 (m-30) cc_final: 0.8009 (m-30) REVERT: O 64 GLU cc_start: 0.8281 (tt0) cc_final: 0.8013 (tt0) REVERT: T 105 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6433 (mp0) outliers start: 77 outliers final: 45 residues processed: 464 average time/residue: 0.8215 time to fit residues: 433.0546 Evaluate side-chains 462 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 402 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 676 ASN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 228 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 58 GLN F 93 ASN I 25 GLN L 86 ASN M 39 GLN M 453 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097014 restraints weight = 28804.243| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.17 r_work: 0.2780 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 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 : 0.004 0.357 28708 Z= 0.152 Angle : 0.684 35.285 38922 Z= 0.301 Chirality : 0.044 0.191 4220 Planarity : 0.005 0.063 4997 Dihedral : 8.981 157.878 4105 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.57 % Allowed : 16.44 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.51 (0.14), residues: 3439 helix: 1.28 (0.14), residues: 1335 sheet: 0.13 (0.26), residues: 377 loop : -0.29 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 286 TYR 0.018 0.002 TYR P 64 PHE 0.015 0.002 PHE J 207 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00339 (28670) covalent geometry : angle 0.56335 (38839) SS BOND : bond 0.00978 ( 1) SS BOND : angle 3.04304 ( 2) hydrogen bonds : bond 0.04950 ( 1143) hydrogen bonds : angle 4.85473 ( 3147) metal coordination : bond 0.06068 ( 36) metal coordination : angle 8.51918 ( 81) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 403 time to evaluate : 0.736 Fit side-chains REVERT: A 29 LYS cc_start: 0.6370 (tttt) cc_final: 0.5480 (mptm) REVERT: A 301 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: A 401 LYS cc_start: 0.7906 (mttt) cc_final: 0.7661 (mtmt) REVERT: B 114 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9241 (pp) REVERT: C 99 GLN cc_start: 0.8375 (pt0) cc_final: 0.8129 (mt0) REVERT: E 51 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8083 (mp-120) REVERT: F 19 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (pp) REVERT: F 35 ASP cc_start: 0.8183 (m-30) cc_final: 0.7709 (m-30) REVERT: F 57 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: G 129 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6736 (mm-30) REVERT: H 73 GLN cc_start: 0.8083 (mm110) cc_final: 0.7584 (mt0) REVERT: H 95 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (tp) REVERT: I 30 GLU cc_start: 0.8748 (pm20) cc_final: 0.8515 (pm20) REVERT: J 214 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8669 (mp) REVERT: K 102 SER cc_start: 0.9007 (t) cc_final: 0.8758 (m) REVERT: L 156 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8124 (mttp) REVERT: M 215 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6343 (tpt) REVERT: M 382 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7696 (mtt180) REVERT: M 643 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.7215 (mtt-85) REVERT: M 676 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.6232 (t0) REVERT: N 8 ARG cc_start: 0.7649 (mmt90) cc_final: 0.7237 (mtt-85) REVERT: O 50 ASP cc_start: 0.8335 (m-30) cc_final: 0.8045 (m-30) REVERT: O 64 GLU cc_start: 0.8332 (tt0) cc_final: 0.8078 (tt0) REVERT: Q 104 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: T 105 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6423 (mp0) outliers start: 77 outliers final: 49 residues processed: 455 average time/residue: 0.8179 time to fit residues: 422.4832 Evaluate side-chains 464 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 400 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 676 ASN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 255 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 193 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 overall best weight: 2.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN E 58 GLN F 93 ASN I 25 GLN M 39 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.096221 restraints weight = 28747.396| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.17 r_work: 0.2766 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.383 28708 Z= 0.167 Angle : 0.702 35.056 38922 Z= 0.313 Chirality : 0.045 0.193 4220 Planarity : 0.005 0.064 4997 Dihedral : 9.023 159.134 4105 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.54 % Allowed : 16.58 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.47 (0.14), residues: 3439 helix: 1.21 (0.14), residues: 1346 sheet: 0.12 (0.26), residues: 377 loop : -0.30 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 138 TYR 0.018 0.002 TYR P 64 PHE 0.016 0.002 PHE J 207 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00376 (28670) covalent geometry : angle 0.58587 (38839) SS BOND : bond 0.01059 ( 1) SS BOND : angle 3.10841 ( 2) hydrogen bonds : bond 0.05221 ( 1143) hydrogen bonds : angle 4.91845 ( 3147) metal coordination : bond 0.06514 ( 36) metal coordination : angle 8.48049 ( 81) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 404 time to evaluate : 1.132 Fit side-chains REVERT: A 29 LYS cc_start: 0.6376 (tttt) cc_final: 0.5470 (mptm) REVERT: A 301 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: A 401 LYS cc_start: 0.7972 (mttt) cc_final: 0.7714 (mtmt) REVERT: B 114 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9247 (pp) REVERT: C 99 GLN cc_start: 0.8384 (pt0) cc_final: 0.8139 (mt0) REVERT: E 37 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8235 (mtp180) REVERT: E 51 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8075 (mp-120) REVERT: F 19 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8676 (pp) REVERT: F 35 ASP cc_start: 0.8151 (m-30) cc_final: 0.7677 (m-30) REVERT: F 57 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: G 111 ASP cc_start: 0.7209 (p0) cc_final: 0.6698 (p0) REVERT: G 129 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: G 132 ASP cc_start: 0.7546 (t0) cc_final: 0.7343 (t70) REVERT: H 73 GLN cc_start: 0.8091 (mm110) cc_final: 0.7572 (mt0) REVERT: I 30 GLU cc_start: 0.8781 (pm20) cc_final: 0.8542 (pm20) REVERT: J 214 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8692 (mp) REVERT: K 102 SER cc_start: 0.9007 (t) cc_final: 0.8752 (m) REVERT: L 156 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: M 215 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6305 (tpt) REVERT: M 643 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: M 676 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.6218 (t0) REVERT: N 8 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7240 (mtt-85) REVERT: O 50 ASP cc_start: 0.8339 (m-30) cc_final: 0.8045 (m-30) REVERT: O 64 GLU cc_start: 0.8343 (tt0) cc_final: 0.8075 (tt0) REVERT: P 231 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.7702 (mpp80) REVERT: Q 104 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: T 105 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6467 (mp0) outliers start: 76 outliers final: 50 residues processed: 455 average time/residue: 0.8099 time to fit residues: 418.6716 Evaluate side-chains 467 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 402 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 676 ASN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 335 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN F 93 ASN I 25 GLN M 39 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.097200 restraints weight = 28602.847| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.17 r_work: 0.2779 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 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 : 0.004 0.341 28708 Z= 0.149 Angle : 0.690 36.764 38922 Z= 0.302 Chirality : 0.044 0.192 4220 Planarity : 0.005 0.063 4997 Dihedral : 8.910 161.468 4105 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 2.41 % Allowed : 16.78 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3439 helix: 1.26 (0.14), residues: 1335 sheet: 0.11 (0.26), residues: 377 loop : -0.30 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 52 TYR 0.018 0.002 TYR P 64 PHE 0.015 0.001 PHE J 207 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00332 (28670) covalent geometry : angle 0.56663 (38839) SS BOND : bond 0.00967 ( 1) SS BOND : angle 3.02537 ( 2) hydrogen bonds : bond 0.04911 ( 1143) hydrogen bonds : angle 4.85923 ( 3147) metal coordination : bond 0.05806 ( 36) metal coordination : angle 8.64487 ( 81) Misc. bond : bond 0.00017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 1.083 Fit side-chains REVERT: A 29 LYS cc_start: 0.6402 (tttt) cc_final: 0.5490 (mptm) REVERT: A 301 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: A 401 LYS cc_start: 0.7899 (mttt) cc_final: 0.7643 (mtmt) REVERT: B 114 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9234 (pp) REVERT: C 99 GLN cc_start: 0.8379 (pt0) cc_final: 0.8126 (mt0) REVERT: E 51 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8077 (mp-120) REVERT: E 100 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8019 (ttt-90) REVERT: F 19 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8682 (pp) REVERT: F 35 ASP cc_start: 0.8151 (m-30) cc_final: 0.7686 (m-30) REVERT: F 57 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: G 111 ASP cc_start: 0.7057 (p0) cc_final: 0.6543 (p0) REVERT: G 129 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: G 132 ASP cc_start: 0.7510 (t0) cc_final: 0.7283 (t70) REVERT: H 73 GLN cc_start: 0.8084 (mm110) cc_final: 0.7590 (mt0) REVERT: I 30 GLU cc_start: 0.8775 (pm20) cc_final: 0.8523 (pm20) REVERT: J 214 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8697 (mp) REVERT: K 102 SER cc_start: 0.9012 (t) cc_final: 0.8760 (m) REVERT: L 156 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8131 (mttp) REVERT: M 215 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6300 (tpt) REVERT: M 643 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.7214 (mtt-85) REVERT: M 676 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6258 (t0) REVERT: N 8 ARG cc_start: 0.7662 (mmt90) cc_final: 0.7247 (mtt-85) REVERT: O 50 ASP cc_start: 0.8304 (m-30) cc_final: 0.8012 (m-30) REVERT: O 64 GLU cc_start: 0.8323 (tt0) cc_final: 0.8064 (tt0) REVERT: P 231 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.7684 (mpp80) REVERT: Q 104 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: T 105 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6455 (mp0) outliers start: 72 outliers final: 50 residues processed: 453 average time/residue: 0.8287 time to fit residues: 424.9182 Evaluate side-chains 467 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 402 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 676 ASN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 306 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 204 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN I 25 GLN M 39 GLN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097533 restraints weight = 28723.767| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.15 r_work: 0.2785 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.324 28708 Z= 0.142 Angle : 0.686 37.144 38922 Z= 0.298 Chirality : 0.044 0.189 4220 Planarity : 0.005 0.063 4997 Dihedral : 8.823 162.564 4105 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.44 % Allowed : 16.78 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.51 (0.14), residues: 3439 helix: 1.28 (0.14), residues: 1335 sheet: 0.11 (0.26), residues: 377 loop : -0.29 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 52 TYR 0.017 0.001 TYR P 64 PHE 0.014 0.001 PHE J 207 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00315 (28670) covalent geometry : angle 0.56022 (38839) SS BOND : bond 0.00919 ( 1) SS BOND : angle 2.98826 ( 2) hydrogen bonds : bond 0.04774 ( 1143) hydrogen bonds : angle 4.82489 ( 3147) metal coordination : bond 0.05517 ( 36) metal coordination : angle 8.68036 ( 81) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12382.58 seconds wall clock time: 210 minutes 47.08 seconds (12647.08 seconds total)