Starting phenix.real_space_refine on Fri Mar 6 08:50:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.map" model { file = "/net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxp_32186/03_2026/7vxp_32186.cif" } resolution = 2.7 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= 0.004 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 10 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18157 2.51 5 N 4951 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28589 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 212 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {' UQ': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.172 49.201 110.876 1.00 38.77 S ATOM 3060 SG CYS A 425 47.492 46.073 116.763 1.00 36.60 S ATOM 2738 SG CYS A 385 44.790 44.827 110.990 1.00 40.09 S ATOM 2699 SG CYS A 379 42.958 49.903 114.875 1.00 40.62 S ATOM 3961 SG CYS B 113 35.721 63.936 75.950 1.00 37.70 S ATOM 3980 SG CYS B 116 41.038 61.799 79.626 1.00 42.28 S ATOM 4003 SG CYS B 119 41.850 64.393 74.021 1.00 41.35 S ATOM 4332 SG CYS B 162 39.401 58.590 74.920 1.00 30.85 S ATOM 4030 SG CYS B 123 47.868 67.125 69.187 1.00 40.94 S ATOM 4256 SG CYS B 152 45.882 65.378 63.432 1.00 26.27 S ATOM 4303 SG CYS B 158 44.082 61.544 68.427 1.00 34.59 S ATOM 4282 SG CYS B 155 50.043 61.888 66.768 1.00 37.50 S ATOM 5724 SG CYS C 166 52.267 65.218 58.997 1.00 32.96 S ATOM 4996 SG CYS C 72 52.628 66.597 52.738 1.00 43.95 S ATOM 4990 SG CYS C 71 58.038 65.014 55.586 1.00 38.13 S ATOM 5494 SG CYS C 136 54.755 70.265 57.777 1.00 34.39 S ATOM 14946 SG CYS M 131 40.642 62.308 91.641 1.00 50.79 S ATOM 14925 SG CYS M 128 44.156 57.717 88.504 1.00 35.78 S ATOM 14986 SG CYS M 137 46.299 61.173 93.709 1.00 26.74 S ATOM 15318 SG CYS M 179 44.826 61.569 104.905 1.00 31.19 S ATOM 15672 SG CYS M 226 41.608 64.249 100.542 1.00 46.04 S ATOM 15342 SG CYS M 182 39.377 64.327 106.648 1.00 34.85 S ATOM 15295 SG CYS M 176 39.218 58.760 103.378 1.00 34.13 S ATOM 14543 SG CYS M 78 56.645 57.205 108.323 1.00 35.69 S ATOM 14644 SG CYS M 92 54.845 59.279 110.801 1.00 47.18 S ATOM 14432 SG CYS M 64 50.323 59.150 108.592 1.00 28.24 S ATOM 14518 SG CYS M 75 51.221 57.480 105.835 1.00 32.12 S ATOM 21481 SG CYS O 135 32.327 31.841 119.716 1.00 53.01 S ATOM 21515 SG CYS O 140 32.284 28.417 120.813 1.00 53.05 S ATOM 21795 SG CYS O 176 36.702 33.255 122.174 1.00 68.27 S ATOM 21818 SG CYS O 180 37.396 30.101 123.372 1.00 56.36 S ATOM 27628 SG CYS T 86 28.766 50.741 84.182 1.00 38.22 S ATOM 27806 SG CYS T 111 29.824 54.251 85.181 1.00 43.87 S Time building chain proxies: 5.71, per 1000 atoms: 0.20 Number of scatterers: 28589 At special positions: 0 Unit cell: (124.607, 142.869, 167.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 10 15.00 Mg 1 11.99 O 5252 8.00 N 4951 7.00 C 18157 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="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="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 30 sheets defined 44.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.893A pdb=" N SER A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.582A pdb=" N GLY A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.590A pdb=" N LYS A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.929A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.578A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.680A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 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 338 through 345 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 382 through 402 removed outlier: 4.331A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 4.062A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.506A 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 207 removed outlier: 5.542A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'C' and resid 42 through 61 removed outlier: 3.619A pdb=" N SER C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 removed outlier: 4.115A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 80 " --> pdb=" O MET C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.701A 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 40 Processing helix chain 'F' and resid 40 through 48 removed outlier: 3.741A pdb=" N LEU F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.814A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 64 through 73 removed outlier: 3.534A pdb=" N GLN H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 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 removed outlier: 3.674A pdb=" N ALA I 63 " --> pdb=" O ARG I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.963A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 5.009A 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: 3.689A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 212 through 220 removed outlier: 3.578A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 285 Processing helix chain 'J' and resid 294 through 307 removed outlier: 3.557A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 323 Processing helix chain 'J' and resid 334 through 339 removed outlier: 3.566A pdb=" N GLY J 339 " --> pdb=" O GLU J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 354 Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.592A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.957A 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 69 through 74 removed outlier: 3.614A pdb=" N THR L 74 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 160 through 165 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.563A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.064A 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: 3.558A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE M 333 " --> pdb=" O MET M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 361 removed outlier: 3.764A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 386 removed outlier: 4.009A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 removed outlier: 3.657A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 458 removed outlier: 3.961A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 3.880A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 482 removed outlier: 4.038A pdb=" N GLN M 482 " --> pdb=" O SER M 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 479 through 482' Processing helix chain 'M' and resid 485 through 504 Processing helix chain 'M' and resid 521 through 528 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.108A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 664 through 673 removed outlier: 3.515A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) 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 removed outlier: 3.621A pdb=" N ALA M 708 " --> pdb=" O SER M 704 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 31 removed outlier: 3.967A pdb=" N GLY N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 removed outlier: 4.158A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 68 Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.615A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.772A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.069A 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 removed outlier: 3.574A pdb=" N GLY O 211 " --> pdb=" O GLU O 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.553A pdb=" N HIS P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 3.814A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG P 168 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 88 through 92 removed outlier: 4.182A pdb=" N HIS Q 92 " --> pdb=" O PRO Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 126 Processing helix chain 'Q' and resid 132 through 140 removed outlier: 3.905A pdb=" N PHE Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.688A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 3.912A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 263 removed outlier: 4.032A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 310 through 314 removed outlier: 3.676A pdb=" N VAL Q 314 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 372 removed outlier: 3.535A pdb=" N LYS Q 372 " --> pdb=" O ARG Q 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 4.154A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 454 Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.694A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 4.909A pdb=" N LYS A 184 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 193 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR A 191 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.447A 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: 6.471A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.370A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 57 removed outlier: 3.501A 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: 5.248A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.494A 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: 6.640A pdb=" N VAL J 80 " --> pdb=" O ILE J 104 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET J 106 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL J 82 " --> pdb=" O MET J 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'J' and resid 226 through 228 removed outlier: 5.949A pdb=" N VAL J 226 " --> pdb=" O TYR J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 126 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.079A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 200 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.768A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA M 339 " --> pdb=" O PHE M 546 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU M 548 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE M 341 " --> pdb=" O LEU M 548 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.864A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'N' and resid 37 through 41 removed outlier: 5.498A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.944A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) 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: 6.928A pdb=" N ARG Q 96 " --> pdb=" O PRO Q 111 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL Q 98 " --> pdb=" O CYS Q 109 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS Q 109 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 107 " (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: 4.410A 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 removed outlier: 6.241A pdb=" N SER T 77 " --> pdb=" O ARG T 119 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 83 through 86 1132 hydrogen bonds defined for protein. 3132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 2.98 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: 11758 1.40 - 1.62: 17145 1.62 - 1.84: 277 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 29260 Sorted by residual: bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C18 UQ Q 501 " pdb=" C19 UQ Q 501 " ideal model delta sigma weight residual 1.336 1.554 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C13 UQ Q 501 " pdb=" C14 UQ Q 501 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C13 UQ J 402 " pdb=" C14 UQ J 402 " ideal model delta sigma weight residual 1.335 1.545 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C8 UQ J 402 " pdb=" C9 UQ J 402 " ideal model delta sigma weight residual 1.334 1.543 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 29255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 39299 3.30 - 6.60: 229 6.60 - 9.90: 56 9.90 - 13.20: 29 13.20 - 16.49: 18 Bond angle restraints: 39631 Sorted by residual: angle pdb=" C GLU J 311 " pdb=" N PRO J 312 " pdb=" CA PRO J 312 " ideal model delta sigma weight residual 119.76 128.63 -8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" N MET Q 197 " pdb=" CA MET Q 197 " pdb=" C MET Q 197 " ideal model delta sigma weight residual 111.36 120.68 -9.32 1.09e+00 8.42e-01 7.31e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.94 -16.20 1.95e+00 2.62e-01 6.88e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.25 -13.41 1.91e+00 2.73e-01 4.90e+01 angle pdb=" C SER J 308 " pdb=" N PRO J 309 " pdb=" CA PRO J 309 " ideal model delta sigma weight residual 119.05 126.71 -7.66 1.11e+00 8.12e-01 4.76e+01 ... (remaining 39626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 17082 34.10 - 68.20: 596 68.20 - 102.31: 40 102.31 - 136.41: 2 136.41 - 170.51: 7 Dihedral angle restraints: 17727 sinusoidal: 7498 harmonic: 10229 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -139.48 53.48 1 1.00e+01 1.00e-02 3.89e+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 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" C2 PLX C 303 " pdb=" O1 PLX C 303 " pdb=" P1 PLX C 303 " pdb=" O3 PLX C 303 " ideal model delta sinusoidal sigma weight residual 310.56 140.05 170.51 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3828 0.074 - 0.147: 416 0.147 - 0.221: 21 0.221 - 0.294: 6 0.294 - 0.368: 7 Chirality restraints: 4278 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 -2.38 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA PHE Q 136 " pdb=" N PHE Q 136 " pdb=" C PHE Q 136 " pdb=" CB PHE Q 136 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+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 2.35 -0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 4275 not shown) Planarity restraints: 5098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.468 2.00e-02 2.50e+03 4.09e-01 2.10e+03 pdb=" C18 UQ J 402 " 0.519 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.410 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.035 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ Q 501 " 0.308 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" C18 UQ Q 501 " -0.583 2.00e-02 2.50e+03 pdb=" C19 UQ Q 501 " 0.238 2.00e-02 2.50e+03 pdb=" C20 UQ Q 501 " 0.022 2.00e-02 2.50e+03 pdb=" C21 UQ Q 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.311 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C13 UQ J 402 " -0.570 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.218 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.068 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.027 2.00e-02 2.50e+03 ... (remaining 5095 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1110 2.72 - 3.26: 27842 3.26 - 3.81: 46911 3.81 - 4.35: 61304 4.35 - 4.90: 102635 Nonbonded interactions: 239802 Sorted by model distance: nonbonded pdb=" OD2 ASP M 295 " pdb=" OG1 THR M 706 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR Q 226 " pdb=" O GLN Q 234 " model vdw 2.189 3.040 nonbonded pdb=" OG SER B 94 " pdb=" OE2 GLU Q 215 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR Q 178 " pdb=" OH TYR Q 214 " model vdw 2.221 3.040 ... (remaining 239797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.640 Find NCS groups from input model: 0.270 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 0.316 29297 Z= 0.382 Angle : 0.895 17.919 39714 Z= 0.422 Chirality : 0.048 0.368 4278 Planarity : 0.015 0.409 5098 Dihedral : 16.615 170.510 11148 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 13.20 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3502 helix: 0.84 (0.14), residues: 1344 sheet: 0.09 (0.26), residues: 386 loop : -0.63 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 52 TYR 0.019 0.001 TYR C 142 PHE 0.015 0.001 PHE Q 204 TRP 0.012 0.001 TRP M 422 HIS 0.005 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00811 (29260) covalent geometry : angle 0.84269 (39631) SS BOND : bond 0.00451 ( 1) SS BOND : angle 2.87554 ( 2) hydrogen bonds : bond 0.15026 ( 1132) hydrogen bonds : angle 6.25584 ( 3132) metal coordination : bond 0.01360 ( 35) metal coordination : angle 6.71664 ( 81) Misc. bond : bond 0.12512 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 392 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 87 LYS cc_start: 0.8816 (mttp) cc_final: 0.8499 (mmmt) REVERT: G 97 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6600 (tptt) REVERT: G 125 GLU cc_start: 0.7140 (tp30) cc_final: 0.6867 (tp30) REVERT: M 441 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7565 (ttp-110) REVERT: N 116 ASN cc_start: 0.8522 (t0) cc_final: 0.8204 (t0) REVERT: Q 145 MET cc_start: 0.9127 (mtt) cc_final: 0.8904 (tpp) REVERT: Q 148 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8506 (pt0) outliers start: 36 outliers final: 28 residues processed: 420 average time/residue: 0.7400 time to fit residues: 355.3587 Evaluate side-chains 410 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 380 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 246 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 457 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN A 451 GLN F 25 GLN F 31 GLN F 62 GLN G 101 ASN H 50 GLN L 109 ASN M 464 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 ASN O 69 ASN O 153 GLN P 51 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.082731 restraints weight = 39492.042| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.74 r_work: 0.2830 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29297 Z= 0.180 Angle : 0.651 20.322 39714 Z= 0.299 Chirality : 0.045 0.204 4278 Planarity : 0.005 0.069 5098 Dihedral : 11.486 169.599 4246 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 2.37 % Allowed : 12.21 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3502 helix: 1.06 (0.14), residues: 1364 sheet: -0.02 (0.25), residues: 395 loop : -0.62 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.021 0.002 TYR J 180 PHE 0.020 0.002 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00432 (29260) covalent geometry : angle 0.57233 (39631) SS BOND : bond 0.00999 ( 1) SS BOND : angle 4.54224 ( 2) hydrogen bonds : bond 0.04949 ( 1132) hydrogen bonds : angle 5.10170 ( 3132) metal coordination : bond 0.01358 ( 35) metal coordination : angle 6.87779 ( 81) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 407 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 43 MET cc_start: 0.7961 (tpp) cc_final: 0.7674 (tpp) REVERT: B 50 MET cc_start: 0.7630 (tpp) cc_final: 0.7360 (tpt) REVERT: E 87 LYS cc_start: 0.8907 (mttp) cc_final: 0.8519 (mmmt) REVERT: F 93 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7347 (t0) REVERT: F 95 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (mp) REVERT: F 96 SER cc_start: 0.7366 (m) cc_final: 0.7037 (p) REVERT: G 125 GLU cc_start: 0.7262 (tp30) cc_final: 0.7049 (tp30) REVERT: J 311 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: L 78 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8540 (ttt-90) REVERT: M 42 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8316 (mmm) REVERT: M 150 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7861 (mtp85) REVERT: M 249 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: M 441 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7737 (ttp-110) REVERT: M 507 THR cc_start: 0.4178 (OUTLIER) cc_final: 0.3868 (m) REVERT: M 530 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7830 (t80) REVERT: M 632 MET cc_start: 0.8180 (ptp) cc_final: 0.7931 (mtm) REVERT: N 133 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8516 (mmtm) REVERT: O 138 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8966 (p) REVERT: O 159 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7708 (mmmt) REVERT: O 195 ASP cc_start: 0.8851 (m-30) cc_final: 0.8574 (m-30) REVERT: Q 308 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8015 (p90) REVERT: T 43 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: T 105 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7147 (tp30) outliers start: 72 outliers final: 27 residues processed: 447 average time/residue: 0.7730 time to fit residues: 394.0819 Evaluate side-chains 421 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 660 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 254 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 141 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN F 31 GLN F 62 GLN G 101 ASN H 50 GLN J 356 HIS L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 558 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN O 153 GLN P 51 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.084856 restraints weight = 39719.472| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.75 r_work: 0.2857 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29297 Z= 0.124 Angle : 0.597 19.084 39714 Z= 0.268 Chirality : 0.042 0.205 4278 Planarity : 0.004 0.065 5098 Dihedral : 10.620 170.465 4212 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.11 % Allowed : 13.69 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3502 helix: 1.21 (0.14), residues: 1368 sheet: -0.12 (0.25), residues: 401 loop : -0.57 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.019 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.010 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00289 (29260) covalent geometry : angle 0.51134 (39631) SS BOND : bond 0.00832 ( 1) SS BOND : angle 3.97016 ( 2) hydrogen bonds : bond 0.04017 ( 1132) hydrogen bonds : angle 4.80226 ( 3132) metal coordination : bond 0.00972 ( 35) metal coordination : angle 6.81300 ( 81) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 405 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7945 (mtm110) REVERT: A 456 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 43 MET cc_start: 0.7938 (tpp) cc_final: 0.7692 (tpp) REVERT: B 50 MET cc_start: 0.7587 (tpp) cc_final: 0.7345 (tpt) REVERT: C 171 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: E 87 LYS cc_start: 0.8902 (mttp) cc_final: 0.8531 (mmmt) REVERT: F 90 THR cc_start: 0.8915 (t) cc_final: 0.8667 (p) REVERT: F 95 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8256 (mp) REVERT: F 96 SER cc_start: 0.7376 (m) cc_final: 0.7063 (p) REVERT: G 84 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8029 (mm) REVERT: G 97 LYS cc_start: 0.7107 (ttpp) cc_final: 0.6588 (tptt) REVERT: G 122 MET cc_start: 0.8387 (mmt) cc_final: 0.8117 (mmm) REVERT: G 125 GLU cc_start: 0.7418 (tp30) cc_final: 0.7135 (tp30) REVERT: G 129 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7522 (tm-30) REVERT: H 30 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (ttpt) REVERT: H 41 ASN cc_start: 0.8131 (p0) cc_final: 0.7894 (p0) REVERT: J 87 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: J 311 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: M 249 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: M 329 MET cc_start: 0.8551 (mmt) cc_final: 0.8349 (mmm) REVERT: M 370 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: M 441 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7700 (ttp-110) REVERT: M 501 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7477 (ttp-170) REVERT: M 507 THR cc_start: 0.4280 (OUTLIER) cc_final: 0.3953 (m) REVERT: M 530 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7928 (t80) REVERT: M 632 MET cc_start: 0.8088 (ptp) cc_final: 0.7830 (mtm) REVERT: N 41 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: N 44 TYR cc_start: 0.8956 (m-80) cc_final: 0.8740 (m-80) REVERT: N 133 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8487 (mmtm) REVERT: O 159 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7704 (mmmt) REVERT: O 195 ASP cc_start: 0.8859 (m-30) cc_final: 0.8582 (m-30) REVERT: O 215 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8552 (mmtm) REVERT: Q 104 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7060 (mt-10) REVERT: Q 308 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7895 (p90) REVERT: T 43 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8848 (tm-30) REVERT: T 107 LYS cc_start: 0.8430 (tttp) cc_final: 0.7841 (ttpm) outliers start: 64 outliers final: 23 residues processed: 451 average time/residue: 0.7603 time to fit residues: 392.2670 Evaluate side-chains 425 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 385 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 138 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 344 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN F 25 GLN F 31 GLN F 62 GLN G 101 ASN H 50 GLN I 25 GLN L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN M 464 GLN M 540 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 51 ASN T 74 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.081817 restraints weight = 39736.505| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.76 r_work: 0.2803 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 29297 Z= 0.231 Angle : 0.671 21.067 39714 Z= 0.311 Chirality : 0.047 0.236 4278 Planarity : 0.005 0.066 5098 Dihedral : 10.625 176.197 4206 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 3.13 % Allowed : 13.46 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3502 helix: 1.02 (0.14), residues: 1372 sheet: -0.22 (0.25), residues: 387 loop : -0.66 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 52 TYR 0.023 0.002 TYR J 180 PHE 0.020 0.002 PHE Q 458 TRP 0.013 0.001 TRP M 510 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00567 (29260) covalent geometry : angle 0.59377 (39631) SS BOND : bond 0.00977 ( 1) SS BOND : angle 4.20425 ( 2) hydrogen bonds : bond 0.05089 ( 1132) hydrogen bonds : angle 4.96128 ( 3132) metal coordination : bond 0.01534 ( 35) metal coordination : angle 6.89548 ( 81) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 388 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7995 (pttp) REVERT: A 359 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8015 (mtm110) REVERT: A 456 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 43 MET cc_start: 0.7925 (tpp) cc_final: 0.7666 (tpp) REVERT: C 171 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: C 188 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7557 (ptmt) REVERT: E 87 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8521 (mmmt) REVERT: E 92 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: F 95 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8061 (mp) REVERT: F 96 SER cc_start: 0.7464 (m) cc_final: 0.7186 (p) REVERT: G 97 LYS cc_start: 0.7512 (ttpp) cc_final: 0.6911 (tptt) REVERT: G 122 MET cc_start: 0.8414 (mmt) cc_final: 0.8162 (mmm) REVERT: G 125 GLU cc_start: 0.7391 (tp30) cc_final: 0.7103 (tp30) REVERT: G 143 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: H 41 ASN cc_start: 0.8164 (p0) cc_final: 0.7926 (p0) REVERT: J 87 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: J 311 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: L 78 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8619 (ttt-90) REVERT: M 39 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: M 42 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8344 (mmm) REVERT: M 249 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: M 370 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: M 441 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7767 (ttp-110) REVERT: M 501 ARG cc_start: 0.7707 (ttt180) cc_final: 0.7412 (ttp-170) REVERT: M 507 THR cc_start: 0.4324 (OUTLIER) cc_final: 0.3994 (m) REVERT: M 509 ASP cc_start: 0.7661 (p0) cc_final: 0.7460 (p0) REVERT: M 530 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7947 (t80) REVERT: M 632 MET cc_start: 0.8283 (ptp) cc_final: 0.8016 (mtm) REVERT: N 133 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (mmtm) REVERT: O 159 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7756 (mmmt) REVERT: O 195 ASP cc_start: 0.8920 (m-30) cc_final: 0.8666 (m-30) REVERT: P 50 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7872 (mmt90) REVERT: P 56 LYS cc_start: 0.8794 (mttm) cc_final: 0.8562 (mtmm) REVERT: Q 308 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8043 (p90) REVERT: Q 323 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8791 (mmm160) REVERT: T 43 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8823 (tm-30) REVERT: T 107 LYS cc_start: 0.8516 (tttp) cc_final: 0.7844 (ttpm) outliers start: 95 outliers final: 36 residues processed: 450 average time/residue: 0.7832 time to fit residues: 403.4091 Evaluate side-chains 430 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 373 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 333 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 274 optimal weight: 0.0770 chunk 249 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 324 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 451 GLN F 25 GLN F 31 GLN F 62 GLN G 101 ASN H 50 GLN I 47 HIS L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN M 464 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.084809 restraints weight = 39314.109| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.75 r_work: 0.2856 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29297 Z= 0.110 Angle : 0.590 18.709 39714 Z= 0.265 Chirality : 0.042 0.219 4278 Planarity : 0.004 0.065 5098 Dihedral : 10.154 179.220 4201 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.27 % Allowed : 14.91 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3502 helix: 1.29 (0.14), residues: 1364 sheet: -0.31 (0.24), residues: 415 loop : -0.54 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 23 TYR 0.019 0.001 TYR J 180 PHE 0.020 0.001 PHE G 126 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00251 (29260) covalent geometry : angle 0.50402 (39631) SS BOND : bond 0.00842 ( 1) SS BOND : angle 3.66608 ( 2) hydrogen bonds : bond 0.03796 ( 1132) hydrogen bonds : angle 4.71971 ( 3132) metal coordination : bond 0.00825 ( 35) metal coordination : angle 6.80478 ( 81) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 398 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8026 (mtm110) REVERT: A 456 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 43 MET cc_start: 0.7851 (tpp) cc_final: 0.7649 (tpp) REVERT: C 171 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: E 87 LYS cc_start: 0.8934 (mttp) cc_final: 0.8505 (mmmt) REVERT: E 92 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8738 (mt-10) REVERT: F 93 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7403 (t0) REVERT: F 95 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7993 (mp) REVERT: F 96 SER cc_start: 0.7457 (m) cc_final: 0.7189 (p) REVERT: G 97 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6916 (tptt) REVERT: G 122 MET cc_start: 0.8334 (mmt) cc_final: 0.8114 (mmm) REVERT: G 125 GLU cc_start: 0.7470 (tp30) cc_final: 0.7162 (tp30) REVERT: G 139 MET cc_start: 0.8231 (mmp) cc_final: 0.7921 (tpt) REVERT: H 41 ASN cc_start: 0.8145 (p0) cc_final: 0.7895 (p0) REVERT: J 311 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: J 365 GLU cc_start: 0.7675 (pm20) cc_final: 0.7448 (pm20) REVERT: J 366 MET cc_start: 0.8831 (ttp) cc_final: 0.8602 (tmm) REVERT: L 78 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (ttt-90) REVERT: M 42 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: M 249 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: M 255 ASP cc_start: 0.8423 (p0) cc_final: 0.8177 (p0) REVERT: M 329 MET cc_start: 0.8568 (mmt) cc_final: 0.8367 (mmm) REVERT: M 370 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: M 441 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7619 (ttp-110) REVERT: M 501 ARG cc_start: 0.7642 (ttt180) cc_final: 0.7424 (ttp-170) REVERT: M 507 THR cc_start: 0.4358 (OUTLIER) cc_final: 0.4065 (m) REVERT: M 509 ASP cc_start: 0.7651 (p0) cc_final: 0.7446 (p0) REVERT: M 530 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7909 (t80) REVERT: M 632 MET cc_start: 0.8067 (ptp) cc_final: 0.7806 (mtm) REVERT: N 41 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: N 44 TYR cc_start: 0.8956 (m-80) cc_final: 0.8723 (m-80) REVERT: O 159 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7700 (mmmt) REVERT: O 195 ASP cc_start: 0.8858 (m-30) cc_final: 0.8557 (m-30) REVERT: P 50 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7865 (mmt90) REVERT: P 56 LYS cc_start: 0.8771 (mttm) cc_final: 0.8497 (mtmm) REVERT: P 161 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8310 (mptt) REVERT: Q 104 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7004 (mt-10) REVERT: Q 308 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7930 (p90) REVERT: Q 323 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8776 (mmm160) REVERT: T 43 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8847 (tm-30) REVERT: T 107 LYS cc_start: 0.8436 (tttp) cc_final: 0.7802 (ttpm) outliers start: 69 outliers final: 25 residues processed: 440 average time/residue: 0.7809 time to fit residues: 393.7597 Evaluate side-chains 427 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 329 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 152 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 25 GLN F 31 GLN F 62 GLN F 76 ASN G 101 ASN H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN M 464 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083572 restraints weight = 39473.776| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.75 r_work: 0.2833 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29297 Z= 0.162 Angle : 0.615 19.771 39714 Z= 0.279 Chirality : 0.044 0.222 4278 Planarity : 0.005 0.063 5098 Dihedral : 10.116 177.310 4201 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 2.30 % Allowed : 15.40 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3502 helix: 1.29 (0.14), residues: 1358 sheet: -0.27 (0.24), residues: 402 loop : -0.55 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 52 TYR 0.020 0.001 TYR J 180 PHE 0.018 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00394 (29260) covalent geometry : angle 0.53339 (39631) SS BOND : bond 0.00927 ( 1) SS BOND : angle 3.72891 ( 2) hydrogen bonds : bond 0.04240 ( 1132) hydrogen bonds : angle 4.73416 ( 3132) metal coordination : bond 0.01078 ( 35) metal coordination : angle 6.78912 ( 81) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 387 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7991 (pttp) REVERT: A 359 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8026 (mtm110) REVERT: A 456 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 171 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: E 87 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8501 (mmmt) REVERT: E 92 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: F 93 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7380 (t0) REVERT: F 95 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8005 (mp) REVERT: F 96 SER cc_start: 0.7468 (m) cc_final: 0.7210 (p) REVERT: G 97 LYS cc_start: 0.7550 (ttpp) cc_final: 0.6938 (tptt) REVERT: G 122 MET cc_start: 0.8357 (mmt) cc_final: 0.8143 (mmm) REVERT: G 125 GLU cc_start: 0.7495 (tp30) cc_final: 0.7202 (tp30) REVERT: H 41 ASN cc_start: 0.8135 (p0) cc_final: 0.7893 (p0) REVERT: J 311 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: J 365 GLU cc_start: 0.7716 (pm20) cc_final: 0.7467 (pm20) REVERT: L 78 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8458 (ttt-90) REVERT: L 148 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8217 (mt-10) REVERT: M 42 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: M 249 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: M 329 MET cc_start: 0.8591 (mmt) cc_final: 0.8390 (mmm) REVERT: M 370 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: M 441 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7701 (ttp-110) REVERT: M 507 THR cc_start: 0.4359 (OUTLIER) cc_final: 0.4037 (m) REVERT: M 509 ASP cc_start: 0.7658 (p0) cc_final: 0.7448 (p0) REVERT: M 530 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8049 (t80) REVERT: M 632 MET cc_start: 0.8142 (ptp) cc_final: 0.7852 (mtm) REVERT: N 132 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8452 (ttpt) REVERT: N 133 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8519 (mmtm) REVERT: O 159 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7708 (mmmt) REVERT: O 195 ASP cc_start: 0.8885 (m-30) cc_final: 0.8610 (m-30) REVERT: P 50 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7849 (mmt90) REVERT: P 161 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8362 (mptt) REVERT: Q 104 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7087 (mt-10) REVERT: Q 308 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7990 (p90) REVERT: Q 323 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8800 (mmm160) REVERT: T 43 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8816 (tm-30) REVERT: T 107 LYS cc_start: 0.8477 (tttp) cc_final: 0.7823 (ttpm) outliers start: 70 outliers final: 34 residues processed: 434 average time/residue: 0.7994 time to fit residues: 397.8087 Evaluate side-chains 429 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 326 optimal weight: 0.9990 chunk 147 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN F 31 GLN F 62 GLN F 76 ASN G 101 ASN H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 558 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 82 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085154 restraints weight = 39279.299| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.75 r_work: 0.2861 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29297 Z= 0.116 Angle : 0.588 18.699 39714 Z= 0.264 Chirality : 0.042 0.228 4278 Planarity : 0.004 0.064 5098 Dihedral : 9.786 168.892 4201 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 2.24 % Allowed : 15.66 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3502 helix: 1.37 (0.14), residues: 1368 sheet: -0.27 (0.25), residues: 403 loop : -0.53 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 52 TYR 0.018 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00270 (29260) covalent geometry : angle 0.50283 (39631) SS BOND : bond 0.00842 ( 1) SS BOND : angle 3.47949 ( 2) hydrogen bonds : bond 0.03687 ( 1132) hydrogen bonds : angle 4.60712 ( 3132) metal coordination : bond 0.00809 ( 35) metal coordination : angle 6.72984 ( 81) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (pttp) REVERT: A 359 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (mtm110) REVERT: A 456 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 171 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: E 87 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8464 (mmmt) REVERT: E 92 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: F 93 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7422 (t0) REVERT: F 95 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8014 (mp) REVERT: F 96 SER cc_start: 0.7493 (m) cc_final: 0.7238 (p) REVERT: G 97 LYS cc_start: 0.7514 (ttpp) cc_final: 0.6928 (tptt) REVERT: G 110 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7463 (mt) REVERT: G 122 MET cc_start: 0.8355 (mmt) cc_final: 0.8151 (mmm) REVERT: G 125 GLU cc_start: 0.7507 (tp30) cc_final: 0.7137 (tp30) REVERT: H 41 ASN cc_start: 0.8119 (p0) cc_final: 0.7866 (p0) REVERT: J 311 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: J 365 GLU cc_start: 0.7676 (pm20) cc_final: 0.7438 (pm20) REVERT: J 366 MET cc_start: 0.8848 (ttp) cc_final: 0.8591 (tmm) REVERT: L 78 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: L 148 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8232 (mt-10) REVERT: M 42 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: M 249 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: M 329 MET cc_start: 0.8577 (mmt) cc_final: 0.8375 (mmm) REVERT: M 370 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: M 441 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7674 (ttp-110) REVERT: M 507 THR cc_start: 0.4177 (OUTLIER) cc_final: 0.3906 (m) REVERT: M 509 ASP cc_start: 0.7636 (p0) cc_final: 0.7421 (p0) REVERT: M 530 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8045 (t80) REVERT: M 632 MET cc_start: 0.8033 (ptp) cc_final: 0.7748 (mtm) REVERT: N 41 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: N 132 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8433 (tttt) REVERT: N 133 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8516 (mmtm) REVERT: O 159 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7666 (mmmt) REVERT: Q 104 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7024 (mt-10) REVERT: Q 308 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7953 (p90) REVERT: Q 323 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8784 (mmm160) REVERT: Q 356 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8756 (pt) REVERT: T 43 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: T 107 LYS cc_start: 0.8447 (tttp) cc_final: 0.7798 (ttpm) outliers start: 68 outliers final: 28 residues processed: 436 average time/residue: 0.7614 time to fit residues: 381.1902 Evaluate side-chains 430 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 380 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 281 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN F 31 GLN F 62 GLN G 101 ASN H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN M 464 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.084880 restraints weight = 39504.572| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.76 r_work: 0.2856 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29297 Z= 0.125 Angle : 0.590 19.081 39714 Z= 0.266 Chirality : 0.043 0.231 4278 Planarity : 0.004 0.062 5098 Dihedral : 9.569 158.826 4200 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.11 % Allowed : 16.32 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3502 helix: 1.41 (0.14), residues: 1367 sheet: -0.24 (0.25), residues: 403 loop : -0.52 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 52 TYR 0.018 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00294 (29260) covalent geometry : angle 0.50871 (39631) SS BOND : bond 0.00875 ( 1) SS BOND : angle 3.49171 ( 2) hydrogen bonds : bond 0.03776 ( 1132) hydrogen bonds : angle 4.58824 ( 3132) metal coordination : bond 0.00866 ( 35) metal coordination : angle 6.60863 ( 81) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 389 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7980 (pttp) REVERT: A 359 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8001 (mtm110) REVERT: A 456 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 43 MET cc_start: 0.7885 (tpp) cc_final: 0.7626 (tpp) REVERT: C 171 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: E 87 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8501 (mmmt) REVERT: F 95 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8051 (mp) REVERT: F 96 SER cc_start: 0.7391 (m) cc_final: 0.7169 (p) REVERT: G 97 LYS cc_start: 0.7542 (ttpp) cc_final: 0.6937 (tptt) REVERT: G 110 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7483 (mt) REVERT: G 125 GLU cc_start: 0.7487 (tp30) cc_final: 0.7104 (tp30) REVERT: H 41 ASN cc_start: 0.8152 (p0) cc_final: 0.7898 (p0) REVERT: J 212 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7602 (tpp-160) REVERT: J 311 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: J 365 GLU cc_start: 0.7687 (pm20) cc_final: 0.7445 (pm20) REVERT: L 78 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8425 (ttt-90) REVERT: L 148 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8235 (mt-10) REVERT: M 42 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: M 249 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: M 329 MET cc_start: 0.8575 (mmt) cc_final: 0.8366 (mmm) REVERT: M 370 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: M 441 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7673 (ttp-110) REVERT: M 507 THR cc_start: 0.4133 (OUTLIER) cc_final: 0.3881 (m) REVERT: M 509 ASP cc_start: 0.7649 (p0) cc_final: 0.7427 (p0) REVERT: M 530 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8012 (t80) REVERT: M 632 MET cc_start: 0.8035 (ptp) cc_final: 0.7754 (mtm) REVERT: N 132 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8414 (ttpt) REVERT: N 133 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8500 (mmtm) REVERT: O 159 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7549 (mmmt) REVERT: P 161 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: Q 104 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6940 (mt-10) REVERT: Q 308 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7932 (p90) REVERT: Q 323 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8813 (mmm160) REVERT: Q 356 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8750 (pt) REVERT: T 43 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8818 (tm-30) REVERT: T 107 LYS cc_start: 0.8419 (tttp) cc_final: 0.7775 (ttpm) outliers start: 64 outliers final: 31 residues processed: 430 average time/residue: 0.7672 time to fit residues: 378.4892 Evaluate side-chains 432 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 381 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 227 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 327 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 25 GLN F 31 GLN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN M 464 GLN M 558 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.083313 restraints weight = 39288.436| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.76 r_work: 0.2834 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29297 Z= 0.152 Angle : 0.614 19.609 39714 Z= 0.279 Chirality : 0.044 0.232 4278 Planarity : 0.005 0.063 5098 Dihedral : 9.468 152.624 4198 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.91 % Allowed : 16.42 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3502 helix: 1.37 (0.14), residues: 1361 sheet: -0.24 (0.25), residues: 395 loop : -0.53 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 52 TYR 0.019 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00366 (29260) covalent geometry : angle 0.53584 (39631) SS BOND : bond 0.00899 ( 1) SS BOND : angle 3.57231 ( 2) hydrogen bonds : bond 0.04071 ( 1132) hydrogen bonds : angle 4.65454 ( 3132) metal coordination : bond 0.01013 ( 35) metal coordination : angle 6.65921 ( 81) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 380 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7990 (pttp) REVERT: A 359 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (mtm110) REVERT: A 456 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 171 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: E 87 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8498 (mmmt) REVERT: F 95 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8065 (mp) REVERT: G 97 LYS cc_start: 0.7600 (ttpp) cc_final: 0.6952 (tptt) REVERT: G 110 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7475 (mt) REVERT: G 122 MET cc_start: 0.8302 (mmm) cc_final: 0.8072 (mmm) REVERT: G 125 GLU cc_start: 0.7309 (tp30) cc_final: 0.7038 (tp30) REVERT: H 41 ASN cc_start: 0.8149 (p0) cc_final: 0.7906 (p0) REVERT: J 212 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7609 (tpp-160) REVERT: J 311 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: J 365 GLU cc_start: 0.7724 (pm20) cc_final: 0.7465 (pm20) REVERT: M 42 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8188 (mmm) REVERT: M 249 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: M 329 MET cc_start: 0.8583 (mmt) cc_final: 0.8380 (mmm) REVERT: M 370 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: M 441 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7604 (ttp-110) REVERT: M 509 ASP cc_start: 0.7639 (p0) cc_final: 0.7434 (p0) REVERT: M 530 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7941 (t80) REVERT: M 632 MET cc_start: 0.8108 (ptp) cc_final: 0.7812 (mtm) REVERT: N 132 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8395 (ttpt) REVERT: N 133 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8530 (mmtm) REVERT: O 138 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8947 (p) REVERT: Q 104 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6997 (mt-10) REVERT: Q 308 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7873 (p90) REVERT: Q 323 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (mmm160) REVERT: Q 356 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8769 (pt) REVERT: T 43 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8790 (tm-30) REVERT: T 107 LYS cc_start: 0.8419 (tttp) cc_final: 0.7769 (ttpm) outliers start: 58 outliers final: 32 residues processed: 420 average time/residue: 0.7826 time to fit residues: 376.7477 Evaluate side-chains 425 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 306 optimal weight: 0.9990 chunk 273 optimal weight: 0.0370 chunk 90 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN F 31 GLN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.083742 restraints weight = 39327.189| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.73 r_work: 0.2844 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29297 Z= 0.133 Angle : 0.603 19.153 39714 Z= 0.273 Chirality : 0.043 0.233 4278 Planarity : 0.004 0.062 5098 Dihedral : 9.299 150.912 4198 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.81 % Allowed : 16.68 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3502 helix: 1.37 (0.14), residues: 1368 sheet: -0.24 (0.25), residues: 395 loop : -0.52 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 52 TYR 0.019 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.010 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00316 (29260) covalent geometry : angle 0.52379 (39631) SS BOND : bond 0.00883 ( 1) SS BOND : angle 3.49043 ( 2) hydrogen bonds : bond 0.03873 ( 1132) hydrogen bonds : angle 4.61937 ( 3132) metal coordination : bond 0.00894 ( 35) metal coordination : angle 6.62142 ( 81) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 377 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7987 (pttp) REVERT: A 359 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8035 (mtm110) REVERT: A 456 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 171 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: E 87 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8464 (mmmt) REVERT: F 95 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8067 (mp) REVERT: G 97 LYS cc_start: 0.7602 (ttpp) cc_final: 0.6951 (tptt) REVERT: G 110 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7451 (mt) REVERT: G 125 GLU cc_start: 0.7436 (tp30) cc_final: 0.7055 (tp30) REVERT: G 139 MET cc_start: 0.8230 (mmp) cc_final: 0.7935 (tpt) REVERT: H 41 ASN cc_start: 0.8147 (p0) cc_final: 0.7900 (p0) REVERT: I 62 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8484 (mt-10) REVERT: J 212 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7610 (tpp-160) REVERT: J 311 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: J 365 GLU cc_start: 0.7721 (pm20) cc_final: 0.7475 (pm20) REVERT: M 42 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8168 (mmm) REVERT: M 249 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: M 329 MET cc_start: 0.8573 (mmt) cc_final: 0.8366 (mmm) REVERT: M 370 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: M 441 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7593 (ttp-110) REVERT: M 509 ASP cc_start: 0.7592 (p0) cc_final: 0.7381 (p0) REVERT: M 530 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.7915 (t80) REVERT: M 632 MET cc_start: 0.8054 (ptp) cc_final: 0.7756 (mtm) REVERT: N 132 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8419 (ttpt) REVERT: N 133 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8530 (mmtm) REVERT: O 138 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8956 (p) REVERT: P 56 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8434 (mtmm) REVERT: Q 104 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6931 (mt-10) REVERT: Q 308 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.7875 (p90) REVERT: Q 323 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8776 (mmm160) REVERT: Q 356 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8782 (pt) REVERT: T 43 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8810 (tm-30) REVERT: T 107 LYS cc_start: 0.8405 (tttp) cc_final: 0.7763 (ttpm) outliers start: 55 outliers final: 32 residues processed: 414 average time/residue: 0.7871 time to fit residues: 373.4354 Evaluate side-chains 425 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 307 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 323 optimal weight: 0.0170 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN F 31 GLN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 558 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN P 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.083980 restraints weight = 39497.900| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.76 r_work: 0.2844 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29297 Z= 0.133 Angle : 0.602 19.188 39714 Z= 0.273 Chirality : 0.043 0.237 4278 Planarity : 0.004 0.062 5098 Dihedral : 9.186 149.973 4198 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 1.94 % Allowed : 16.45 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3502 helix: 1.37 (0.14), residues: 1369 sheet: -0.21 (0.25), residues: 389 loop : -0.52 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 52 TYR 0.018 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00316 (29260) covalent geometry : angle 0.52330 (39631) SS BOND : bond 0.00868 ( 1) SS BOND : angle 3.43796 ( 2) hydrogen bonds : bond 0.03870 ( 1132) hydrogen bonds : angle 4.61723 ( 3132) metal coordination : bond 0.00885 ( 35) metal coordination : angle 6.60289 ( 81) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10568.47 seconds wall clock time: 180 minutes 29.75 seconds (10829.75 seconds total)