Starting phenix.real_space_refine on Fri Mar 6 06:06:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxu_32188/03_2026/7vxu_32188.map" } resolution = 2.8 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 9 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17704 2.51 5 N 4878 2.21 5 O 5156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27965 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 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: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1244 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} 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: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 678 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 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: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2356 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "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 2706 SG CYS A 382 48.821 49.379 102.225 1.00 59.61 S ATOM 3048 SG CYS A 425 48.248 45.883 107.885 1.00 58.89 S ATOM 2726 SG CYS A 385 45.609 45.076 102.168 1.00 59.05 S ATOM 2687 SG CYS A 379 43.837 50.207 106.254 1.00 63.64 S ATOM 3949 SG CYS B 113 37.230 66.608 68.123 1.00 53.35 S ATOM 3968 SG CYS B 116 42.398 63.877 71.648 1.00 52.06 S ATOM 3991 SG CYS B 119 43.288 66.719 66.224 1.00 46.31 S ATOM 4320 SG CYS B 162 40.525 60.975 66.848 1.00 49.80 S ATOM 4018 SG CYS B 123 49.414 69.443 61.490 1.00 51.87 S ATOM 4244 SG CYS B 152 47.340 67.834 55.711 1.00 45.96 S ATOM 4291 SG CYS B 158 45.348 64.122 60.447 1.00 51.25 S ATOM 4270 SG CYS B 155 51.571 64.249 58.872 1.00 57.54 S ATOM 5708 SG CYS C 166 53.314 67.661 51.375 1.00 50.88 S ATOM 4978 SG CYS C 71 58.133 67.670 47.277 1.00 65.70 S ATOM 4984 SG CYS C 72 54.789 69.495 45.338 1.00 56.72 S ATOM 4978 SG CYS C 71 58.133 67.670 47.277 1.00 65.70 S ATOM 5478 SG CYS C 136 56.303 72.336 50.082 1.00 54.16 S ATOM 14516 SG CYS M 131 41.921 63.590 83.826 1.00 59.47 S ATOM 14495 SG CYS M 128 45.361 59.128 80.426 1.00 60.60 S ATOM 14556 SG CYS M 137 47.626 62.327 85.797 1.00 59.40 S ATOM 14888 SG CYS M 179 46.345 62.045 96.907 1.00 54.14 S ATOM 15242 SG CYS M 226 43.181 65.133 92.765 1.00 58.99 S ATOM 14912 SG CYS M 182 41.034 65.149 98.826 1.00 54.24 S ATOM 14865 SG CYS M 176 40.543 59.686 95.251 1.00 58.79 S ATOM 14113 SG CYS M 78 57.846 57.107 100.188 1.00 65.59 S ATOM 14214 SG CYS M 92 56.268 59.081 102.751 1.00 71.16 S ATOM 14002 SG CYS M 64 51.820 59.245 100.313 1.00 58.16 S ATOM 14088 SG CYS M 75 52.644 57.481 97.331 1.00 57.91 S ATOM 21051 SG CYS O 135 32.287 32.334 110.281 1.00 68.86 S ATOM 21085 SG CYS O 140 32.060 28.913 111.076 1.00 76.95 S ATOM 21365 SG CYS O 176 36.739 33.970 112.888 1.00 81.42 S ATOM 21388 SG CYS O 180 36.941 30.458 112.875 1.00 74.21 S ATOM 27146 SG CYS T 86 29.830 53.337 75.982 1.00 59.72 S ATOM 27324 SG CYS T 111 30.769 56.487 76.826 1.00 67.23 S Time building chain proxies: 5.68, per 1000 atoms: 0.20 Number of scatterers: 27965 At special positions: 0 Unit cell: (125.681, 140.72, 157.907, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 9 15.00 Mg 1 11.99 O 5156 8.00 N 4878 7.00 C 17704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 29 sheets defined 44.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.509A pdb=" N ARG A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.601A pdb=" N ILE A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.726A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.794A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 179 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 218 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.776A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.065A 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 329 through 333 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: 3.784A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.919A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.534A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 209 removed outlier: 5.776A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.890A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 113 through 124 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 196 Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.644A 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 removed outlier: 3.544A pdb=" N LYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 48 removed outlier: 7.474A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 83 through 97 Processing helix chain 'G' and resid 75 through 89 removed outlier: 3.698A pdb=" N LYS G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.718A pdb=" N GLU G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.803A 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 65 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.687A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 75 removed outlier: 3.657A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 98 Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.877A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 211 through 219 removed outlier: 3.847A pdb=" N ASN J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 316 through 324 removed outlier: 3.650A pdb=" N GLU J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 339 Processing helix chain 'J' and resid 344 through 354 removed outlier: 4.116A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) 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: 3.601A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 119 through 123 removed outlier: 3.617A pdb=" N SER L 122 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 119 through 123' 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 57 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.463A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.715A pdb=" N ARG M 184 " --> pdb=" O THR M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 removed outlier: 4.024A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.096A 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 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 360 Processing helix chain 'M' and resid 381 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 4.234A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (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: 4.029A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 4.050A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU M 468 " --> pdb=" O GLN M 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 483 removed outlier: 4.040A pdb=" N ARG M 483 " --> pdb=" O SER M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 520 through 528 removed outlier: 4.782A pdb=" N ALA M 524 " --> pdb=" O ALA M 520 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 664 through 672 Processing helix chain 'M' and resid 690 through 694 Processing helix chain 'M' and resid 698 through 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.549A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.878A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 70 removed outlier: 3.871A pdb=" N TYR O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.680A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.739A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 157 removed outlier: 3.636A pdb=" N LEU O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 52 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 174 removed outlier: 4.136A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 4.081A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 134 through 140 removed outlier: 3.699A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 4.038A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 4.140A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.878A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.862A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 310 through 314 Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 374 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 4.091A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.750A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 removed outlier: 3.563A pdb=" N VAL Q 461 " --> pdb=" O VAL Q 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.669A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 removed outlier: 3.512A pdb=" N GLU T 73 " --> pdb=" O ASP T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 94 removed outlier: 3.504A pdb=" N LEU T 93 " --> pdb=" O GLY T 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.816A pdb=" N ASN A 185 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A 191 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA A 154 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 198 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 156 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (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: 6.213A 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: 6.500A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.392A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 58 removed outlier: 6.543A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.673A 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: 5.210A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP P 113 " --> pdb=" O ASN P 131 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.289A 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: 6.569A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB4, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.211A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 7.165A 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=AB6, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB8, first strand: chain 'M' and resid 246 through 251 Processing sheet with id=AB9, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.575A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.273A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.815A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.953A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.722A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC7, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.761A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AC9, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD1, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD2, first strand: chain 'T' and resid 83 through 86 1117 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 3.24 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: 11508 1.40 - 1.62: 16744 1.62 - 1.84: 273 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 28605 Sorted by residual: bond pdb=" C2B NDP J 401 " pdb=" C3B NDP J 401 " ideal model delta sigma weight residual 1.552 1.235 0.317 3.50e-02 8.16e+02 8.18e+01 bond pdb=" C5N NDP J 401 " pdb=" C6N NDP J 401 " ideal model delta sigma weight residual 1.337 1.550 -0.213 2.40e-02 1.74e+03 7.90e+01 bond pdb=" CA7 CDL N 201 " pdb=" OA8 CDL N 201 " ideal model delta sigma weight residual 1.334 1.429 -0.095 1.10e-02 8.26e+03 7.53e+01 bond pdb=" CZ 2MR Q 118 " pdb=" NH1 2MR Q 118 " ideal model delta sigma weight residual 1.281 1.438 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C2N NDP J 401 " pdb=" C3N NDP J 401 " ideal model delta sigma weight residual 1.357 1.552 -0.195 2.50e-02 1.60e+03 6.09e+01 ... (remaining 28600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 38481 3.36 - 6.73: 204 6.73 - 10.09: 40 10.09 - 13.45: 11 13.45 - 16.82: 6 Bond angle restraints: 38742 Sorted by residual: angle pdb=" C ASP L 119 " pdb=" N PRO L 120 " pdb=" CA PRO L 120 " ideal model delta sigma weight residual 119.05 131.03 -11.98 1.11e+00 8.12e-01 1.16e+02 angle pdb=" C MET C 124 " pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 120.31 128.50 -8.19 9.80e-01 1.04e+00 6.99e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.24 -15.50 1.95e+00 2.62e-01 6.29e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.81 -13.97 1.91e+00 2.73e-01 5.32e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.67 7.79 1.17e+00 7.36e-01 4.46e+01 ... (remaining 38737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 16613 33.07 - 66.15: 675 66.15 - 99.22: 47 99.22 - 132.30: 6 132.30 - 165.37: 2 Dihedral angle restraints: 17343 sinusoidal: 7281 harmonic: 10062 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 -143.73 57.73 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CA SER O 224 " pdb=" C SER O 224 " pdb=" N CYS O 225 " pdb=" CA CYS O 225 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA5 CDL N 201 " pdb=" CA4 CDL N 201 " pdb=" OA6 CDL N 201 " pdb=" CA6 CDL N 201 " ideal model delta sinusoidal sigma weight residual 168.24 2.87 165.37 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 17340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3737 0.071 - 0.142: 453 0.142 - 0.213: 11 0.213 - 0.284: 6 0.284 - 0.355: 5 Chirality restraints: 4212 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 -2.39 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA PHE Q 174 " pdb=" N PHE Q 174 " pdb=" C PHE Q 174 " pdb=" CB PHE Q 174 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+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 2.34 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 4209 not shown) Planarity restraints: 4989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.158 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" C3N NDP J 401 " 0.423 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.046 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.305 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.115 2.00e-02 2.50e+03 2.05e-01 4.18e+02 pdb=" C2N NDP J 401 " 0.119 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.042 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C5N NDP J 401 " 0.073 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.073 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.042 2.00e-02 2.50e+03 ... (remaining 4986 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1877 2.73 - 3.28: 27550 3.28 - 3.82: 46437 3.82 - 4.36: 57852 4.36 - 4.90: 99410 Nonbonded interactions: 233126 Sorted by model distance: nonbonded pdb=" CB GLU C 126 " pdb=" CD PRO C 127 " model vdw 2.193 3.840 nonbonded pdb=" NZ LYS F 64 " pdb=" OD1 ASN F 76 " model vdw 2.207 3.120 nonbonded pdb=" O2' FMN A 502 " pdb=" O4' FMN A 502 " model vdw 2.226 3.040 nonbonded pdb=" O PRO M 472 " pdb=" NE1 TRP M 510 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU A 208 " pdb=" OG1 THR A 210 " model vdw 2.234 3.040 ... (remaining 233121 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: 2.980 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.007 0.326 28643 Z= 0.334 Angle : 0.918 70.335 38825 Z= 0.380 Chirality : 0.046 0.355 4212 Planarity : 0.006 0.265 4989 Dihedral : 16.758 165.369 10868 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 1.34 % Allowed : 17.00 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.49 (0.14), residues: 3439 helix: 1.19 (0.14), residues: 1328 sheet: 0.37 (0.26), residues: 390 loop : -0.31 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 89 TYR 0.019 0.001 TYR C 142 PHE 0.021 0.001 PHE J 288 TRP 0.015 0.001 TRP M 422 HIS 0.005 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00623 (28605) covalent geometry : angle 0.71786 (38742) SS BOND : bond 0.00399 ( 1) SS BOND : angle 1.82010 ( 2) hydrogen bonds : bond 0.14889 ( 1117) hydrogen bonds : angle 6.30502 ( 3108) metal coordination : bond 0.02141 ( 36) metal coordination : angle 12.53591 ( 81) Misc. bond : bond 0.32576 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 392 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: E 87 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (ttmt) REVERT: G 120 MET cc_start: 0.8496 (mtm) cc_final: 0.7890 (mtm) REVERT: H 96 ARG cc_start: 0.7679 (tmm-80) cc_final: 0.7384 (mtp85) REVERT: O 185 MET cc_start: 0.8795 (ppp) cc_final: 0.8381 (ppp) REVERT: P 222 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8004 (mm-30) REVERT: W 5 LYS cc_start: 0.7686 (tppt) cc_final: 0.7076 (ttpt) outliers start: 40 outliers final: 29 residues processed: 422 average time/residue: 0.7326 time to fit residues: 354.3878 Evaluate side-chains 402 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 372 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 387 GLU Chi-restraints excluded: chain T residue 41 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN F 25 GLN J 154 GLN L 88 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.084953 restraints weight = 39703.332| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.03 r_work: 0.2881 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 28643 Z= 0.140 Angle : 0.798 70.385 38825 Z= 0.281 Chirality : 0.043 0.155 4212 Planarity : 0.005 0.066 4989 Dihedral : 9.543 150.103 4083 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.24 % Allowed : 15.96 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.59 (0.14), residues: 3439 helix: 1.37 (0.15), residues: 1332 sheet: 0.37 (0.26), residues: 398 loop : -0.34 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 74 TYR 0.021 0.001 TYR P 64 PHE 0.013 0.001 PHE L 164 TRP 0.013 0.001 TRP M 422 HIS 0.005 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00334 (28605) covalent geometry : angle 0.53571 (38742) SS BOND : bond 0.00685 ( 1) SS BOND : angle 2.14194 ( 2) hydrogen bonds : bond 0.04302 ( 1117) hydrogen bonds : angle 5.00694 ( 3108) metal coordination : bond 0.02869 ( 36) metal coordination : angle 12.95292 ( 81) Misc. bond : bond 0.00159 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 395 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 68 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: E 110 THR cc_start: 0.8808 (t) cc_final: 0.8549 (m) REVERT: G 76 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7254 (mp) REVERT: G 143 GLU cc_start: 0.6753 (pt0) cc_final: 0.6534 (pt0) REVERT: H 96 ARG cc_start: 0.7893 (tmm-80) cc_final: 0.7546 (mtm110) REVERT: I 51 ASN cc_start: 0.8507 (t0) cc_final: 0.8255 (t0) REVERT: J 79 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: J 336 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: K 94 SER cc_start: 0.8947 (t) cc_final: 0.8702 (p) REVERT: M 188 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8501 (mt-10) REVERT: P 222 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8142 (mm-30) REVERT: Q 215 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8894 (tm-30) REVERT: W 5 LYS cc_start: 0.7544 (tppt) cc_final: 0.6966 (ttpp) outliers start: 67 outliers final: 22 residues processed: 433 average time/residue: 0.7551 time to fit residues: 374.9081 Evaluate side-chains 389 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 329 MET Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 308 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 191 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN G 103 HIS J 154 GLN J 171 ASN K 75 ASN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082440 restraints weight = 39908.943| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.03 r_work: 0.2836 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 28643 Z= 0.187 Angle : 0.788 68.373 38825 Z= 0.288 Chirality : 0.045 0.160 4212 Planarity : 0.005 0.059 4989 Dihedral : 8.753 155.821 4039 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.98 % Allowed : 17.03 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.50 (0.14), residues: 3439 helix: 1.31 (0.14), residues: 1342 sheet: 0.33 (0.27), residues: 386 loop : -0.40 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 82 TYR 0.019 0.001 TYR P 64 PHE 0.014 0.002 PHE Q 204 TRP 0.012 0.001 TRP M 422 HIS 0.004 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00460 (28605) covalent geometry : angle 0.54910 (38742) SS BOND : bond 0.00697 ( 1) SS BOND : angle 2.24467 ( 2) hydrogen bonds : bond 0.04525 ( 1117) hydrogen bonds : angle 4.90332 ( 3108) metal coordination : bond 0.03784 ( 36) metal coordination : angle 12.38144 ( 81) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 377 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8622 (mtpt) REVERT: A 456 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: B 68 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7964 (ttp80) REVERT: F 26 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7311 (mtm-85) REVERT: G 123 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: G 129 GLU cc_start: 0.7336 (tp30) cc_final: 0.7042 (tp30) REVERT: G 143 GLU cc_start: 0.6972 (pt0) cc_final: 0.6690 (pt0) REVERT: I 30 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: I 51 ASN cc_start: 0.8500 (t0) cc_final: 0.8189 (t0) REVERT: J 79 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7870 (tp40) REVERT: J 316 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5908 (mmt-90) REVERT: J 336 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: L 108 GLU cc_start: 0.8720 (tt0) cc_final: 0.8497 (tt0) REVERT: M 188 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8454 (mt-10) REVERT: M 535 GLU cc_start: 0.7903 (tp30) cc_final: 0.7617 (tp30) REVERT: P 247 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: Q 185 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8498 (tpt) REVERT: Q 215 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8716 (tm-30) REVERT: W 5 LYS cc_start: 0.7509 (tppt) cc_final: 0.6986 (tppp) outliers start: 89 outliers final: 44 residues processed: 432 average time/residue: 0.7616 time to fit residues: 377.2893 Evaluate side-chains 417 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 316 ARG Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 281 ILE Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 247 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 7 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 132 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 157 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 156 optimal weight: 0.0050 chunk 40 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 418 GLN E 70 ASN J 154 GLN J 171 ASN M 142 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN P 180 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084460 restraints weight = 39160.391| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.03 r_work: 0.2879 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 28643 Z= 0.109 Angle : 0.738 64.708 38825 Z= 0.258 Chirality : 0.042 0.145 4212 Planarity : 0.004 0.065 4989 Dihedral : 8.196 159.272 4034 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.58 % Allowed : 18.21 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.63 (0.14), residues: 3439 helix: 1.44 (0.14), residues: 1343 sheet: 0.42 (0.27), residues: 389 loop : -0.37 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 74 TYR 0.016 0.001 TYR P 64 PHE 0.011 0.001 PHE B 175 TRP 0.012 0.001 TRP M 422 HIS 0.004 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00252 (28605) covalent geometry : angle 0.48942 (38742) SS BOND : bond 0.00650 ( 1) SS BOND : angle 2.07503 ( 2) hydrogen bonds : bond 0.03610 ( 1117) hydrogen bonds : angle 4.67449 ( 3108) metal coordination : bond 0.02316 ( 36) metal coordination : angle 12.09476 ( 81) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 1.103 Fit side-chains REVERT: A 456 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: B 68 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7889 (ttp80) REVERT: B 76 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.6889 (t80) REVERT: C 79 MET cc_start: 0.9013 (ttt) cc_final: 0.8637 (ttt) REVERT: C 188 LYS cc_start: 0.8350 (pttt) cc_final: 0.8137 (pttt) REVERT: E 119 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8324 (mp) REVERT: F 26 ARG cc_start: 0.7936 (mpt-90) cc_final: 0.7292 (mtm-85) REVERT: F 90 THR cc_start: 0.8547 (t) cc_final: 0.8076 (p) REVERT: G 143 GLU cc_start: 0.6870 (pt0) cc_final: 0.6561 (pt0) REVERT: H 29 THR cc_start: 0.8760 (m) cc_final: 0.8447 (m) REVERT: H 96 ARG cc_start: 0.7909 (tmm-80) cc_final: 0.7497 (mtm110) REVERT: I 51 ASN cc_start: 0.8575 (t0) cc_final: 0.8222 (t0) REVERT: J 79 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: J 143 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8270 (t0) REVERT: J 336 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: M 118 GLU cc_start: 0.8970 (tt0) cc_final: 0.8710 (tt0) REVERT: M 188 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8479 (mt-10) REVERT: M 535 GLU cc_start: 0.7936 (tp30) cc_final: 0.7508 (tp30) REVERT: P 247 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: Q 185 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8471 (tpt) REVERT: Q 215 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8695 (tm-30) REVERT: W 5 LYS cc_start: 0.7677 (tppt) cc_final: 0.7243 (tppp) outliers start: 77 outliers final: 36 residues processed: 440 average time/residue: 0.7538 time to fit residues: 380.3382 Evaluate side-chains 409 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 247 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 91 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN E 70 ASN F 93 ASN J 154 GLN J 171 ASN L 86 ASN M 74 ASN M 142 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 669 ASN O 69 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 = 0.103734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.080515 restraints weight = 39769.872| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.02 r_work: 0.2815 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 28643 Z= 0.222 Angle : 0.794 65.061 38825 Z= 0.298 Chirality : 0.046 0.164 4212 Planarity : 0.005 0.073 4989 Dihedral : 8.273 161.205 4034 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.38 % Allowed : 18.27 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.42 (0.14), residues: 3439 helix: 1.26 (0.14), residues: 1342 sheet: 0.25 (0.26), residues: 388 loop : -0.46 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 74 TYR 0.021 0.002 TYR P 64 PHE 0.015 0.002 PHE N 55 TRP 0.013 0.001 TRP L 166 HIS 0.004 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00550 (28605) covalent geometry : angle 0.56940 (38742) SS BOND : bond 0.00784 ( 1) SS BOND : angle 2.49978 ( 2) hydrogen bonds : bond 0.04731 ( 1117) hydrogen bonds : angle 4.86128 ( 3108) metal coordination : bond 0.04341 ( 36) metal coordination : angle 12.12264 ( 81) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 1.075 Fit side-chains REVERT: B 68 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: B 76 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 110 GLU cc_start: 0.8714 (tt0) cc_final: 0.8363 (tt0) REVERT: C 79 MET cc_start: 0.8993 (ttt) cc_final: 0.8654 (ttt) REVERT: F 17 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8028 (mmt90) REVERT: F 26 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: G 129 GLU cc_start: 0.7601 (tp30) cc_final: 0.7212 (tp30) REVERT: G 143 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: I 51 ASN cc_start: 0.8758 (t0) cc_final: 0.8365 (t0) REVERT: J 79 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: J 316 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.6022 (mmt-90) REVERT: J 320 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: J 336 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: M 188 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8407 (mt-10) REVERT: M 535 GLU cc_start: 0.7944 (tp30) cc_final: 0.7611 (tp30) REVERT: P 161 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8804 (tppp) REVERT: P 247 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: Q 185 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8605 (tpt) REVERT: Q 215 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8793 (tm-30) outliers start: 101 outliers final: 50 residues processed: 428 average time/residue: 0.7509 time to fit residues: 367.4932 Evaluate side-chains 423 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 316 ARG Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain P residue 247 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 62 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 273 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN H 110 ASN J 171 ASN M 142 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081905 restraints weight = 39650.889| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.03 r_work: 0.2838 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 28643 Z= 0.152 Angle : 0.760 64.890 38825 Z= 0.274 Chirality : 0.043 0.150 4212 Planarity : 0.005 0.061 4989 Dihedral : 8.037 162.267 4034 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.88 % Allowed : 19.28 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.47 (0.14), residues: 3439 helix: 1.34 (0.14), residues: 1336 sheet: 0.25 (0.27), residues: 386 loop : -0.46 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.019 0.001 TYR P 64 PHE 0.012 0.001 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.004 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00369 (28605) covalent geometry : angle 0.52298 (38742) SS BOND : bond 0.00732 ( 1) SS BOND : angle 2.29929 ( 2) hydrogen bonds : bond 0.04116 ( 1117) hydrogen bonds : angle 4.75533 ( 3108) metal coordination : bond 0.03276 ( 36) metal coordination : angle 12.08390 ( 81) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 371 time to evaluate : 0.990 Fit side-chains REVERT: A 129 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: A 226 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8650 (mtpt) REVERT: B 68 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7935 (ttp80) REVERT: B 76 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.6994 (t80) REVERT: C 79 MET cc_start: 0.8988 (ttt) cc_final: 0.8723 (ttt) REVERT: F 26 ARG cc_start: 0.7922 (mpt-90) cc_final: 0.7267 (mtm-85) REVERT: G 129 GLU cc_start: 0.7527 (tp30) cc_final: 0.7168 (tp30) REVERT: G 137 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7743 (mttp) REVERT: G 143 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6566 (pt0) REVERT: I 30 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: I 51 ASN cc_start: 0.8755 (t0) cc_final: 0.8355 (t0) REVERT: J 79 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7955 (tp40) REVERT: J 320 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: J 336 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: M 118 GLU cc_start: 0.8968 (tt0) cc_final: 0.8709 (tt0) REVERT: M 188 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8407 (mt-10) REVERT: M 535 GLU cc_start: 0.7951 (tp30) cc_final: 0.7638 (tp30) REVERT: N 9 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5340 (ttp-110) REVERT: O 231 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3474 (mm) REVERT: P 161 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8810 (tppp) REVERT: P 247 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: Q 215 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8701 (tm-30) REVERT: W 5 LYS cc_start: 0.7640 (tppt) cc_final: 0.7038 (ttpp) outliers start: 86 outliers final: 47 residues processed: 422 average time/residue: 0.7614 time to fit residues: 367.0016 Evaluate side-chains 419 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 359 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain P residue 247 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 7 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 203 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 159 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082558 restraints weight = 39383.592| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.01 r_work: 0.2843 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 28643 Z= 0.139 Angle : 0.745 62.044 38825 Z= 0.271 Chirality : 0.043 0.146 4212 Planarity : 0.004 0.057 4989 Dihedral : 7.801 163.677 4034 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.91 % Allowed : 19.51 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.51 (0.14), residues: 3439 helix: 1.38 (0.14), residues: 1336 sheet: 0.26 (0.26), residues: 391 loop : -0.43 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.019 0.001 TYR P 64 PHE 0.012 0.001 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.004 0.001 HIS N 87 Details of bonding type rmsd covalent geometry : bond 0.00337 (28605) covalent geometry : angle 0.51816 (38742) SS BOND : bond 0.00713 ( 1) SS BOND : angle 2.26308 ( 2) hydrogen bonds : bond 0.03902 ( 1117) hydrogen bonds : angle 4.69102 ( 3108) metal coordination : bond 0.03004 ( 36) metal coordination : angle 11.74026 ( 81) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 379 time to evaluate : 1.157 Fit side-chains REVERT: A 129 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: A 226 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: B 68 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7914 (ttp80) REVERT: B 76 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 79 MET cc_start: 0.9021 (ttt) cc_final: 0.8729 (ttt) REVERT: C 86 MET cc_start: 0.8549 (ptm) cc_final: 0.8264 (ptm) REVERT: C 188 LYS cc_start: 0.8439 (pttt) cc_final: 0.8214 (pttt) REVERT: F 26 ARG cc_start: 0.7916 (mpt-90) cc_final: 0.7355 (mtm-85) REVERT: F 90 THR cc_start: 0.8517 (t) cc_final: 0.8050 (p) REVERT: G 129 GLU cc_start: 0.7509 (tp30) cc_final: 0.7161 (tp30) REVERT: G 143 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: I 30 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: I 51 ASN cc_start: 0.8751 (t0) cc_final: 0.8347 (t0) REVERT: J 79 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: J 320 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: J 336 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: M 118 GLU cc_start: 0.8975 (tt0) cc_final: 0.8713 (tt0) REVERT: M 188 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8413 (mt-10) REVERT: M 535 GLU cc_start: 0.7951 (tp30) cc_final: 0.7650 (tp30) REVERT: N 8 ARG cc_start: 0.4772 (mmp-170) cc_final: 0.4158 (mtm110) REVERT: N 9 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.5379 (ttp-110) REVERT: N 67 GLU cc_start: 0.8338 (tt0) cc_final: 0.7471 (tm-30) REVERT: O 231 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3450 (mm) REVERT: P 222 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8115 (mm-30) REVERT: Q 215 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8686 (tm-30) REVERT: W 5 LYS cc_start: 0.7648 (tppt) cc_final: 0.7122 (ttpp) outliers start: 87 outliers final: 49 residues processed: 433 average time/residue: 0.7367 time to fit residues: 364.8385 Evaluate side-chains 424 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 364 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 59 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 49 optimal weight: 0.0370 chunk 24 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 ASN J 171 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082648 restraints weight = 39828.888| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.04 r_work: 0.2842 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 28643 Z= 0.150 Angle : 0.746 61.212 38825 Z= 0.274 Chirality : 0.043 0.148 4212 Planarity : 0.004 0.053 4989 Dihedral : 7.712 164.760 4034 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 2.61 % Allowed : 19.98 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.50 (0.14), residues: 3439 helix: 1.37 (0.14), residues: 1336 sheet: 0.25 (0.26), residues: 391 loop : -0.44 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.020 0.001 TYR P 64 PHE 0.012 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.004 0.001 HIS N 87 Details of bonding type rmsd covalent geometry : bond 0.00365 (28605) covalent geometry : angle 0.52498 (38742) SS BOND : bond 0.00731 ( 1) SS BOND : angle 2.27799 ( 2) hydrogen bonds : bond 0.04003 ( 1117) hydrogen bonds : angle 4.71250 ( 3108) metal coordination : bond 0.03118 ( 36) metal coordination : angle 11.61428 ( 81) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 374 time to evaluate : 1.089 Fit side-chains REVERT: B 68 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7916 (ttp80) REVERT: B 76 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 79 MET cc_start: 0.9011 (ttt) cc_final: 0.8794 (ttt) REVERT: C 86 MET cc_start: 0.8541 (ptm) cc_final: 0.8262 (ptm) REVERT: F 26 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7180 (mtm-85) REVERT: F 90 THR cc_start: 0.8506 (t) cc_final: 0.8054 (p) REVERT: G 123 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7255 (mt-10) REVERT: G 129 GLU cc_start: 0.7506 (tp30) cc_final: 0.7226 (tp30) REVERT: G 143 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: H 66 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (mttp) REVERT: I 30 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: I 51 ASN cc_start: 0.8775 (t0) cc_final: 0.8362 (t0) REVERT: J 79 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: J 320 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: J 336 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: M 118 GLU cc_start: 0.8978 (tt0) cc_final: 0.8748 (tt0) REVERT: M 188 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8416 (mt-10) REVERT: M 535 GLU cc_start: 0.7967 (tp30) cc_final: 0.7670 (tp30) REVERT: N 8 ARG cc_start: 0.4746 (mmp-170) cc_final: 0.4138 (mtm110) REVERT: N 9 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5349 (ttp-110) REVERT: N 67 GLU cc_start: 0.8319 (tt0) cc_final: 0.7446 (tm-30) REVERT: N 136 GLU cc_start: 0.8553 (mp0) cc_final: 0.8208 (pm20) REVERT: P 222 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8095 (mm-30) REVERT: Q 215 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8727 (tm-30) REVERT: W 5 LYS cc_start: 0.7684 (tppt) cc_final: 0.7191 (ttpp) outliers start: 78 outliers final: 55 residues processed: 425 average time/residue: 0.7477 time to fit residues: 363.4711 Evaluate side-chains 426 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 361 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 242 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 305 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 287 optimal weight: 0.0060 chunk 218 optimal weight: 0.9990 chunk 296 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN J 171 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084606 restraints weight = 39558.698| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.01 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 28643 Z= 0.112 Angle : 0.732 59.259 38825 Z= 0.266 Chirality : 0.042 0.143 4212 Planarity : 0.004 0.049 4989 Dihedral : 7.533 165.826 4034 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.11 % Allowed : 20.65 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.59 (0.14), residues: 3439 helix: 1.46 (0.15), residues: 1338 sheet: 0.31 (0.26), residues: 393 loop : -0.40 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.019 0.001 TYR P 64 PHE 0.011 0.001 PHE B 175 TRP 0.013 0.001 TRP M 422 HIS 0.006 0.001 HIS N 87 Details of bonding type rmsd covalent geometry : bond 0.00263 (28605) covalent geometry : angle 0.51086 (38742) SS BOND : bond 0.00667 ( 1) SS BOND : angle 2.11083 ( 2) hydrogen bonds : bond 0.03613 ( 1117) hydrogen bonds : angle 4.63270 ( 3108) metal coordination : bond 0.02380 ( 36) metal coordination : angle 11.48804 ( 81) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 372 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: B 76 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.6999 (t80) REVERT: C 79 MET cc_start: 0.8994 (ttt) cc_final: 0.8777 (ttt) REVERT: C 86 MET cc_start: 0.8635 (ptm) cc_final: 0.8282 (ptm) REVERT: F 90 THR cc_start: 0.8452 (t) cc_final: 0.7988 (p) REVERT: G 123 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7233 (mt-10) REVERT: G 129 GLU cc_start: 0.7481 (tp30) cc_final: 0.7192 (tp30) REVERT: G 139 MET cc_start: 0.7681 (tpt) cc_final: 0.7459 (tpt) REVERT: G 143 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: I 30 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: I 51 ASN cc_start: 0.8768 (t0) cc_final: 0.8356 (t0) REVERT: J 79 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7906 (tp40) REVERT: J 220 MET cc_start: 0.7483 (mtm) cc_final: 0.7233 (mtm) REVERT: J 233 LYS cc_start: 0.7430 (mttp) cc_final: 0.7039 (mttp) REVERT: J 320 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: J 336 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: M 188 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8412 (mt-10) REVERT: M 535 GLU cc_start: 0.7954 (tp30) cc_final: 0.7492 (tp30) REVERT: N 8 ARG cc_start: 0.4714 (mmp-170) cc_final: 0.4113 (mtm110) REVERT: N 9 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.5294 (ttp-110) REVERT: N 67 GLU cc_start: 0.8305 (tt0) cc_final: 0.7433 (tm-30) REVERT: N 136 GLU cc_start: 0.8548 (mp0) cc_final: 0.8170 (pm20) REVERT: P 222 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8099 (mm-30) REVERT: Q 81 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8293 (m) REVERT: Q 107 ARG cc_start: 0.8712 (mmt180) cc_final: 0.8479 (mmt180) REVERT: Q 215 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8700 (tm-30) REVERT: Q 260 GLU cc_start: 0.8366 (tp30) cc_final: 0.7517 (tp30) REVERT: W 5 LYS cc_start: 0.7669 (tppt) cc_final: 0.7215 (ttpp) outliers start: 63 outliers final: 40 residues processed: 416 average time/residue: 0.7292 time to fit residues: 347.1695 Evaluate side-chains 416 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 367 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 290 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN J 154 GLN J 171 ASN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.083517 restraints weight = 39477.173| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.03 r_work: 0.2865 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 28643 Z= 0.126 Angle : 0.733 58.080 38825 Z= 0.269 Chirality : 0.042 0.144 4212 Planarity : 0.004 0.049 4989 Dihedral : 7.474 166.706 4034 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.21 % Allowed : 20.72 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.59 (0.14), residues: 3439 helix: 1.45 (0.15), residues: 1342 sheet: 0.28 (0.26), residues: 391 loop : -0.39 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 323 TYR 0.019 0.001 TYR P 64 PHE 0.012 0.001 PHE L 164 TRP 0.021 0.001 TRP M 285 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00302 (28605) covalent geometry : angle 0.52089 (38742) SS BOND : bond 0.00705 ( 1) SS BOND : angle 2.17697 ( 2) hydrogen bonds : bond 0.03714 ( 1117) hydrogen bonds : angle 4.62753 ( 3108) metal coordination : bond 0.02668 ( 36) metal coordination : angle 11.28717 ( 81) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8629 (mtpt) REVERT: A 456 GLN cc_start: 0.7209 (mt0) cc_final: 0.6927 (mp10) REVERT: B 68 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7881 (ttp80) REVERT: B 76 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7024 (t80) REVERT: C 79 MET cc_start: 0.9001 (ttt) cc_final: 0.8787 (ttt) REVERT: C 86 MET cc_start: 0.8607 (ptm) cc_final: 0.8242 (ptt) REVERT: F 62 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7789 (mt0) REVERT: F 90 THR cc_start: 0.8383 (t) cc_final: 0.7916 (p) REVERT: G 123 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7206 (mt-10) REVERT: G 129 GLU cc_start: 0.7491 (tp30) cc_final: 0.7183 (tp30) REVERT: G 143 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6576 (pt0) REVERT: H 66 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7954 (mttp) REVERT: I 30 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: I 51 ASN cc_start: 0.8799 (t0) cc_final: 0.8389 (t0) REVERT: J 79 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: J 220 MET cc_start: 0.7499 (mtm) cc_final: 0.7117 (mtm) REVERT: J 233 LYS cc_start: 0.7414 (mttp) cc_final: 0.7054 (mttp) REVERT: J 320 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: J 336 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: K 70 ASN cc_start: 0.7523 (p0) cc_final: 0.6437 (t0) REVERT: M 188 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8398 (mt-10) REVERT: M 535 GLU cc_start: 0.7906 (tp30) cc_final: 0.7438 (tp30) REVERT: N 8 ARG cc_start: 0.4729 (mmp-170) cc_final: 0.4124 (mtm110) REVERT: N 9 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.5306 (ttp-110) REVERT: N 67 GLU cc_start: 0.8332 (tt0) cc_final: 0.7451 (tm-30) REVERT: N 136 GLU cc_start: 0.8547 (mp0) cc_final: 0.8162 (pm20) REVERT: O 42 ARG cc_start: 0.8340 (mtt90) cc_final: 0.8066 (ttm110) REVERT: P 222 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8073 (mm-30) REVERT: Q 81 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8287 (m) REVERT: Q 215 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8683 (tm-30) REVERT: W 5 LYS cc_start: 0.7639 (tppt) cc_final: 0.7196 (ttpp) outliers start: 66 outliers final: 42 residues processed: 414 average time/residue: 0.7434 time to fit residues: 352.2368 Evaluate side-chains 421 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 332 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 285 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 302 optimal weight: 0.1980 chunk 252 optimal weight: 0.9980 chunk 186 optimal weight: 0.1980 chunk 189 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 154 GLN J 171 ASN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.084333 restraints weight = 39403.504| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.01 r_work: 0.2861 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 28643 Z= 0.160 Angle : 0.830 59.192 38825 Z= 0.363 Chirality : 0.045 1.072 4212 Planarity : 0.005 0.082 4989 Dihedral : 7.457 166.717 4032 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.04 % Allowed : 20.95 % Favored : 77.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.88 % 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: 0.59 (0.14), residues: 3439 helix: 1.46 (0.15), residues: 1342 sheet: 0.27 (0.26), residues: 391 loop : -0.40 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 74 TYR 0.019 0.001 TYR P 64 PHE 0.012 0.001 PHE L 164 TRP 0.017 0.001 TRP M 285 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00350 (28605) covalent geometry : angle 0.65090 (38742) SS BOND : bond 0.00697 ( 1) SS BOND : angle 2.16922 ( 2) hydrogen bonds : bond 0.03702 ( 1117) hydrogen bonds : angle 4.62676 ( 3108) metal coordination : bond 0.02649 ( 36) metal coordination : angle 11.29061 ( 81) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9976.78 seconds wall clock time: 170 minutes 15.12 seconds (10215.12 seconds total)