Starting phenix.real_space_refine on Fri Mar 6 07:58:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwj_32154/03_2026/7vwj_32154.map" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17740 2.51 5 N 4888 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 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: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "M" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "Q" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "T" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.429 48.388 103.805 1.00 16.11 S ATOM 3048 SG CYS A 425 47.504 45.275 109.599 1.00 19.70 S ATOM 2726 SG CYS A 385 45.103 44.079 103.907 1.00 17.82 S ATOM 2687 SG CYS A 379 43.070 49.357 107.612 1.00 19.58 S ATOM 3949 SG CYS B 113 38.673 63.554 68.362 1.00 12.32 S ATOM 3968 SG CYS B 116 43.575 61.092 72.350 1.00 11.19 S ATOM 3991 SG CYS B 119 44.931 63.473 66.706 1.00 9.95 S ATOM 4320 SG CYS B 162 41.960 57.948 67.536 1.00 9.49 S ATOM 4018 SG CYS B 123 51.025 65.886 62.305 1.00 9.90 S ATOM 4244 SG CYS B 152 49.352 64.103 56.411 1.00 12.55 S ATOM 4291 SG CYS B 158 47.084 60.649 61.499 1.00 9.09 S ATOM 4270 SG CYS B 155 53.165 60.389 60.050 1.00 12.84 S ATOM 5712 SG CYS C 166 55.798 63.585 52.496 1.00 13.00 S ATOM 4984 SG CYS C 72 56.883 64.912 46.015 1.00 13.04 S ATOM 4978 SG CYS C 71 60.981 62.570 48.541 1.00 13.21 S ATOM 5482 SG CYS C 136 58.571 68.253 50.965 1.00 10.19 S ATOM 14538 SG CYS M 131 42.636 61.685 84.429 1.00 13.04 S ATOM 14517 SG CYS M 128 46.106 56.820 81.400 1.00 14.08 S ATOM 14578 SG CYS M 137 48.173 60.204 86.586 1.00 10.86 S ATOM 14910 SG CYS M 179 46.354 60.778 97.744 1.00 11.77 S ATOM 15264 SG CYS M 226 43.399 63.500 93.229 1.00 11.55 S ATOM 14934 SG CYS M 182 40.968 63.772 99.240 1.00 14.47 S ATOM 14887 SG CYS M 176 40.552 58.230 95.892 1.00 12.32 S ATOM 14135 SG CYS M 78 57.556 55.662 101.742 1.00 13.12 S ATOM 14236 SG CYS M 92 55.797 57.991 104.006 1.00 15.24 S ATOM 14024 SG CYS M 64 51.465 58.018 101.714 1.00 12.00 S ATOM 14110 SG CYS M 75 52.497 56.057 98.778 1.00 12.54 S ATOM 21073 SG CYS O 135 31.370 32.095 111.852 1.00 39.57 S ATOM 21107 SG CYS O 140 31.270 28.781 113.195 1.00 41.04 S ATOM 21387 SG CYS O 176 35.908 33.524 114.824 1.00 39.29 S ATOM 21410 SG CYS O 180 36.051 30.076 115.485 1.00 44.56 S ATOM 27168 SG CYS T 86 30.372 50.873 76.412 1.00 17.61 S ATOM 27346 SG CYS T 111 31.908 54.310 77.351 1.00 17.92 S Time building chain proxies: 5.95, per 1000 atoms: 0.21 Number of scatterers: 28748 At special positions: 0 Unit cell: (126.219, 138.035, 160.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 11 15.00 Mg 1 11.99 O 5891 8.00 N 4888 7.00 C 17740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 32 sheets defined 45.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.602A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.635A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.721A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.506A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.755A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.781A 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: 3.503A pdb=" N VAL B 67 " --> pdb=" O TRP B 63 " (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: 5.880A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 61 removed outlier: 3.519A pdb=" N SER C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.958A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.533A pdb=" N SER C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.874A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.713A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 48 removed outlier: 6.252A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 97 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.876A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.806A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.701A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 4.870A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.775A 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: 3.712A pdb=" N ASN J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) removed outlier: 3.547A 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 Processing helix chain 'J' and resid 334 through 339 Processing helix chain 'J' and resid 344 through 354 removed outlier: 4.053A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.951A 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 75 through 81 removed outlier: 4.063A pdb=" N HIS K 78 " --> pdb=" O ASN K 75 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.265A pdb=" N GLY L 66 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 159 through 165 removed outlier: 3.683A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 57 removed outlier: 3.597A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.518A 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 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.069A 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 removed outlier: 3.640A pdb=" N ARG M 299 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.501A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.803A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 458 removed outlier: 3.903A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 3.973A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 528 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 556 through 560 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.057A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 3.528A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) 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 16 Processing helix chain 'N' and resid 19 through 31 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.523A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 69 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.626A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.808A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 3.836A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 51 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 4.061A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.737A 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 133 through 140 removed outlier: 4.093A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.747A 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: 4.040A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.564A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.795A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 310 through 314 removed outlier: 3.699A pdb=" N VAL Q 314 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 372 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 3.987A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.779A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.571A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 6.494A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 291 Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.262A pdb=" N LYS B 39 " --> pdb=" O ILE Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.059A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.279A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 58 Processing sheet with id=AA9, first strand: chain 'I' and resid 67 through 69 removed outlier: 6.566A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU P 111 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.563A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.330A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.394A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.501A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.350A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.997A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 169 through 174 removed outlier: 3.730A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.818A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC9, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.508A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD2, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD3, first strand: chain 'T' and resid 30 through 31 removed outlier: 4.091A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD5, first strand: chain 'T' and resid 83 through 86 1163 hydrogen bonds defined for protein. 3219 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: 5.40 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 11556 1.41 - 1.63: 16771 1.63 - 1.85: 274 1.85 - 2.08: 1 2.08 - 2.30: 80 Bond restraints: 28682 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.635 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CB7 CDL I 201 " pdb=" OB8 CDL I 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 28677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 38599 3.35 - 6.71: 199 6.71 - 10.06: 36 10.06 - 13.42: 11 13.42 - 16.77: 7 Bond angle restraints: 38852 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.51 -16.77 1.95e+00 2.62e-01 7.37e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.43 -14.59 1.91e+00 2.73e-01 5.80e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.33 -9.00 1.32e+00 5.72e-01 4.64e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.28 -8.95 1.32e+00 5.72e-01 4.59e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.64 7.82 1.17e+00 7.36e-01 4.50e+01 ... (remaining 38847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 17022 34.41 - 68.83: 344 68.83 - 103.24: 48 103.24 - 137.65: 6 137.65 - 172.06: 3 Dihedral angle restraints: 17423 sinusoidal: 7360 harmonic: 10063 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -138.56 52.56 1 1.00e+01 1.00e-02 3.76e+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 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA CYS O 225 " pdb=" C CYS O 225 " pdb=" N GLU O 226 " pdb=" CA GLU O 226 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 17420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3767 0.072 - 0.144: 436 0.144 - 0.215: 11 0.215 - 0.287: 3 0.287 - 0.359: 3 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+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 2.32 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C2B NDP J 401 " pdb=" C1B NDP J 401 " pdb=" C3B NDP J 401 " pdb=" O2B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4217 not shown) Planarity restraints: 4998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.059 2.00e-02 2.50e+03 2.20e-01 6.08e+02 pdb=" C3N NDP J 401 " 0.396 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.072 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.236 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.116 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" C2N NDP J 401 " 0.121 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.122 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " 0.065 2.00e-02 2.50e+03 9.46e-02 8.96e+01 pdb=" C5N NDP J 401 " -0.116 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.117 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.066 2.00e-02 2.50e+03 ... (remaining 4995 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 470 2.55 - 3.14: 22169 3.14 - 3.73: 48227 3.73 - 4.31: 71702 4.31 - 4.90: 113101 Nonbonded interactions: 255669 Sorted by model distance: nonbonded pdb=" O GLY J 208 " pdb=" OD1 ASP J 211 " model vdw 1.965 3.040 nonbonded pdb=" O1N NAI A 503 " pdb=" O HOH A 601 " model vdw 2.012 3.040 nonbonded pdb=" OG1 THR Q 178 " pdb=" OH TYR Q 214 " model vdw 2.096 3.040 nonbonded pdb=" O GLU C 126 " pdb=" OH TYR J 89 " model vdw 2.102 3.040 nonbonded pdb=" OH TYR J 68 " pdb=" OE2 GLU J 210 " model vdw 2.132 3.040 ... (remaining 255664 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: 12.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.010 0.807 28722 Z= 0.742 Angle : 0.844 40.734 38935 Z= 0.365 Chirality : 0.045 0.359 4220 Planarity : 0.006 0.220 4998 Dihedral : 14.831 172.065 10948 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % 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: 0.65 (0.14), residues: 3439 helix: 1.18 (0.14), residues: 1322 sheet: 0.52 (0.26), residues: 402 loop : -0.09 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 74 TYR 0.061 0.001 TYR C 142 PHE 0.017 0.001 PHE L 164 TRP 0.037 0.001 TRP J 108 HIS 0.006 0.001 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00735 (28682) covalent geometry : angle 0.72348 (38852) SS BOND : bond 0.00510 ( 1) SS BOND : angle 2.05779 ( 2) hydrogen bonds : bond 0.15640 ( 1163) hydrogen bonds : angle 6.22122 ( 3219) metal coordination : bond 0.03645 ( 36) metal coordination : angle 9.54350 ( 81) Misc. bond : bond 0.64789 ( 3) *********************** 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 508 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 504 time to evaluate : 1.168 Fit side-chains REVERT: A 63 TYR cc_start: 0.8291 (t80) cc_final: 0.7969 (t80) REVERT: A 292 MET cc_start: 0.8050 (tpt) cc_final: 0.7664 (tpt) REVERT: A 356 VAL cc_start: 0.8464 (m) cc_final: 0.8180 (t) REVERT: J 345 LEU cc_start: 0.8790 (tp) cc_final: 0.8565 (tm) REVERT: M 39 GLN cc_start: 0.7873 (tt0) cc_final: 0.7641 (tt0) REVERT: N 25 ARG cc_start: 0.7879 (ttt180) cc_final: 0.6799 (ttm170) REVERT: T 64 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7299 (pm20) outliers start: 4 outliers final: 0 residues processed: 506 average time/residue: 0.8106 time to fit residues: 464.7922 Evaluate side-chains 418 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN F 31 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN Q 160 ASN W 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102865 restraints weight = 32850.419| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.19 r_work: 0.2931 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 28722 Z= 0.152 Angle : 0.713 39.305 38935 Z= 0.298 Chirality : 0.044 0.187 4220 Planarity : 0.005 0.071 4998 Dihedral : 10.310 166.260 4087 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.04 % Allowed : 7.41 % Favored : 90.55 % 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: 0.65 (0.14), residues: 3439 helix: 1.19 (0.14), residues: 1339 sheet: 0.43 (0.26), residues: 382 loop : -0.09 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 74 TYR 0.045 0.002 TYR C 142 PHE 0.019 0.002 PHE N 55 TRP 0.014 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00344 (28682) covalent geometry : angle 0.56304 (38852) SS BOND : bond 0.00836 ( 1) SS BOND : angle 2.73500 ( 2) hydrogen bonds : bond 0.04845 ( 1163) hydrogen bonds : angle 5.17280 ( 3219) metal coordination : bond 0.05080 ( 36) metal coordination : angle 9.59382 ( 81) Misc. bond : bond 0.00227 ( 3) *********************** 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 488 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 427 time to evaluate : 1.170 Fit side-chains REVERT: A 268 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: A 292 MET cc_start: 0.8205 (tpt) cc_final: 0.7882 (tpt) REVERT: A 333 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: E 111 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: F 25 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: G 84 LEU cc_start: 0.8421 (mm) cc_final: 0.8215 (mm) REVERT: G 146 ASP cc_start: 0.7087 (m-30) cc_final: 0.6875 (m-30) REVERT: H 60 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8135 (mtmt) REVERT: L 69 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: L 73 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: M 39 GLN cc_start: 0.8250 (tt0) cc_final: 0.8003 (tt0) REVERT: M 688 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: N 25 ARG cc_start: 0.7755 (ttt180) cc_final: 0.6553 (ttm170) REVERT: N 101 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7520 (ptmt) REVERT: O 103 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7834 (pt0) REVERT: O 166 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7293 (p0) REVERT: P 63 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: P 144 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8775 (mtmt) REVERT: Q 205 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7511 (tm-30) outliers start: 61 outliers final: 21 residues processed: 456 average time/residue: 0.7803 time to fit residues: 404.6376 Evaluate side-chains 430 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 397 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 193 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 196 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 299 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN C 123 GLN F 31 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105362 restraints weight = 32962.482| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.19 r_work: 0.2963 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 28722 Z= 0.109 Angle : 0.676 44.921 38935 Z= 0.265 Chirality : 0.042 0.174 4220 Planarity : 0.004 0.058 4998 Dihedral : 9.450 160.263 4087 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 9.68 % Favored : 88.11 % 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: 0.75 (0.14), residues: 3439 helix: 1.39 (0.14), residues: 1340 sheet: 0.25 (0.26), residues: 377 loop : -0.07 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 269 TYR 0.024 0.001 TYR C 143 PHE 0.016 0.001 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00237 (28682) covalent geometry : angle 0.50030 (38852) SS BOND : bond 0.00649 ( 1) SS BOND : angle 2.42455 ( 2) hydrogen bonds : bond 0.03883 ( 1163) hydrogen bonds : angle 4.87837 ( 3219) metal coordination : bond 0.03223 ( 36) metal coordination : angle 9.97001 ( 81) Misc. bond : bond 0.00043 ( 3) *********************** 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 491 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 425 time to evaluate : 1.170 Fit side-chains REVERT: A 63 TYR cc_start: 0.8117 (t80) cc_final: 0.7706 (t80) REVERT: A 333 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: E 111 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: F 25 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: G 84 LEU cc_start: 0.8397 (mm) cc_final: 0.8114 (mm) REVERT: G 146 ASP cc_start: 0.7137 (m-30) cc_final: 0.6934 (m-30) REVERT: H 60 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7938 (mtmt) REVERT: J 286 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6460 (mmt180) REVERT: J 318 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7771 (tttp) REVERT: L 69 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: M 513 MET cc_start: 0.8449 (tpt) cc_final: 0.8215 (tpt) REVERT: M 551 ASP cc_start: 0.8782 (m-30) cc_final: 0.8533 (m-30) REVERT: M 647 GLU cc_start: 0.8560 (tt0) cc_final: 0.8347 (tt0) REVERT: N 25 ARG cc_start: 0.7759 (ttt180) cc_final: 0.6630 (ttm170) REVERT: N 101 LYS cc_start: 0.7814 (ptpp) cc_final: 0.7534 (ptmt) REVERT: O 103 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7912 (tt0) REVERT: O 166 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7331 (p0) REVERT: P 63 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: P 144 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8655 (mtmt) REVERT: Q 205 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: T 64 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7826 (mp0) outliers start: 66 outliers final: 24 residues processed: 462 average time/residue: 0.7701 time to fit residues: 405.0642 Evaluate side-chains 435 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 399 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain J residue 318 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 3 optimal weight: 8.9990 chunk 338 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 246 optimal weight: 0.0000 chunk 64 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A 418 GLN A 436 GLN C 123 GLN F 31 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN H 71 GLN I 9 GLN J 79 GLN K 79 HIS L 86 ASN L 109 ASN M 39 GLN ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN O 69 ASN P 82 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097197 restraints weight = 32673.213| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.22 r_work: 0.2831 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.468 28722 Z= 0.282 Angle : 0.786 31.990 38935 Z= 0.356 Chirality : 0.051 0.217 4220 Planarity : 0.006 0.077 4998 Dihedral : 9.948 177.911 4087 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 10.42 % Favored : 86.54 % 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: 0.30 (0.14), residues: 3439 helix: 0.95 (0.14), residues: 1334 sheet: 0.30 (0.26), residues: 365 loop : -0.34 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 138 TYR 0.032 0.002 TYR C 143 PHE 0.027 0.003 PHE N 55 TRP 0.015 0.002 TRP M 422 HIS 0.015 0.002 HIS Q 183 Details of bonding type rmsd covalent geometry : bond 0.00686 (28682) covalent geometry : angle 0.67785 (38852) SS BOND : bond 0.01146 ( 1) SS BOND : angle 3.15381 ( 2) hydrogen bonds : bond 0.05937 ( 1163) hydrogen bonds : angle 5.27034 ( 3219) metal coordination : bond 0.08118 ( 36) metal coordination : angle 8.73750 ( 81) Misc. bond : bond 0.00202 ( 3) *********************** 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 485 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 394 time to evaluate : 1.024 Fit side-chains REVERT: A 333 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 448 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 455 LEU cc_start: 0.8011 (mp) cc_final: 0.7745 (tm) REVERT: E 111 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: F 25 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: G 84 LEU cc_start: 0.8412 (mm) cc_final: 0.8122 (mm) REVERT: G 146 ASP cc_start: 0.7168 (m-30) cc_final: 0.6941 (m-30) REVERT: H 60 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8001 (mtmt) REVERT: J 286 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6688 (mmt180) REVERT: J 318 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7637 (tttp) REVERT: L 69 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: L 149 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: M 98 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8449 (ttpp) REVERT: N 25 ARG cc_start: 0.7864 (ttt180) cc_final: 0.6639 (ttm170) REVERT: N 47 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7835 (mmtm) REVERT: N 101 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7743 (ptmt) REVERT: O 72 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: O 166 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7286 (p0) REVERT: P 63 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: Q 104 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: Q 205 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: T 64 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: W 27 ARG cc_start: 0.7397 (ttp80) cc_final: 0.6732 (ttp80) outliers start: 91 outliers final: 45 residues processed: 447 average time/residue: 0.8011 time to fit residues: 406.8687 Evaluate side-chains 438 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 376 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain J residue 318 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 228 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 329 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 310 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN C 123 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101918 restraints weight = 32720.952| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.20 r_work: 0.2916 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.215 28722 Z= 0.122 Angle : 0.699 46.730 38935 Z= 0.278 Chirality : 0.043 0.176 4220 Planarity : 0.005 0.062 4998 Dihedral : 9.301 169.034 4087 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.50 % Allowed : 12.22 % Favored : 85.28 % 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: 1.19 (0.14), residues: 1342 sheet: 0.04 (0.25), residues: 387 loop : -0.21 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 74 TYR 0.016 0.001 TYR J 180 PHE 0.016 0.001 PHE L 164 TRP 0.014 0.001 TRP M 422 HIS 0.007 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00276 (28682) covalent geometry : angle 0.52263 (38852) SS BOND : bond 0.00703 ( 1) SS BOND : angle 2.56010 ( 2) hydrogen bonds : bond 0.04109 ( 1163) hydrogen bonds : angle 4.93477 ( 3219) metal coordination : bond 0.03785 ( 36) metal coordination : angle 10.19882 ( 81) Misc. bond : bond 0.00083 ( 3) *********************** 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 478 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 1.100 Fit side-chains REVERT: A 129 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: A 333 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: E 111 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: F 25 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: G 84 LEU cc_start: 0.8394 (mm) cc_final: 0.8090 (mm) REVERT: G 146 ASP cc_start: 0.7148 (m-30) cc_final: 0.6931 (m-30) REVERT: H 60 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7909 (mtmt) REVERT: H 73 GLN cc_start: 0.8340 (mm110) cc_final: 0.8093 (mt0) REVERT: I 70 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7335 (tmt) REVERT: J 286 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6617 (mmt180) REVERT: L 69 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: L 149 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: M 98 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8356 (ttpp) REVERT: N 25 ARG cc_start: 0.7802 (ttt180) cc_final: 0.6589 (ttm170) REVERT: N 101 LYS cc_start: 0.7910 (ptpp) cc_final: 0.7643 (ptmt) REVERT: O 56 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6699 (p) REVERT: O 103 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7974 (pt0) REVERT: O 166 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7319 (p0) REVERT: P 63 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: P 144 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8805 (mtmt) REVERT: Q 104 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: Q 205 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: T 64 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7711 (mp0) outliers start: 75 outliers final: 36 residues processed: 450 average time/residue: 0.7856 time to fit residues: 402.3122 Evaluate side-chains 435 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 188 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 209 optimal weight: 0.0770 chunk 70 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 245 optimal weight: 0.0980 chunk 252 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN F 76 ASN G 103 HIS H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105465 restraints weight = 32677.790| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.17 r_work: 0.2961 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 28722 Z= 0.105 Angle : 0.673 46.203 38935 Z= 0.261 Chirality : 0.042 0.169 4220 Planarity : 0.004 0.058 4998 Dihedral : 8.863 169.591 4087 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.57 % Allowed : 12.72 % Favored : 84.71 % 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: 0.70 (0.14), residues: 3439 helix: 1.44 (0.14), residues: 1334 sheet: 0.01 (0.26), residues: 387 loop : -0.12 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 538 TYR 0.013 0.001 TYR J 180 PHE 0.014 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 0.00228 (28682) covalent geometry : angle 0.49227 (38852) SS BOND : bond 0.00618 ( 1) SS BOND : angle 2.37830 ( 2) hydrogen bonds : bond 0.03579 ( 1163) hydrogen bonds : angle 4.71906 ( 3219) metal coordination : bond 0.03044 ( 36) metal coordination : angle 10.05891 ( 81) Misc. bond : bond 0.00073 ( 3) *********************** 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 478 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 401 time to evaluate : 0.926 Fit side-chains REVERT: A 333 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: A 455 LEU cc_start: 0.8122 (mp) cc_final: 0.7854 (tm) REVERT: E 69 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8039 (pttm) REVERT: F 25 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: G 84 LEU cc_start: 0.8387 (mm) cc_final: 0.8069 (mm) REVERT: H 60 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7913 (mtmt) REVERT: J 286 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6566 (mmt180) REVERT: L 69 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: M 98 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8335 (ttpp) REVERT: M 551 ASP cc_start: 0.8739 (m-30) cc_final: 0.8515 (m-30) REVERT: N 25 ARG cc_start: 0.7733 (ttt180) cc_final: 0.6545 (ttm170) REVERT: N 101 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7551 (ptmt) REVERT: O 56 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6553 (p) REVERT: O 103 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7890 (pt0) REVERT: O 166 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7301 (p0) REVERT: P 63 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: P 144 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8767 (mtmt) REVERT: Q 205 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: T 64 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7693 (mp0) outliers start: 77 outliers final: 29 residues processed: 449 average time/residue: 0.7654 time to fit residues: 391.1678 Evaluate side-chains 425 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 384 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 301 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN E 51 GLN F 76 ASN H 71 GLN I 9 GLN K 79 HIS M 540 ASN N 52 ASN P 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101691 restraints weight = 32622.562| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.20 r_work: 0.2912 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.283 28722 Z= 0.138 Angle : 0.677 39.345 38935 Z= 0.280 Chirality : 0.043 0.181 4220 Planarity : 0.005 0.055 4998 Dihedral : 8.964 175.827 4087 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 13.29 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3439 helix: 1.36 (0.14), residues: 1340 sheet: 0.04 (0.26), residues: 387 loop : -0.15 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.019 0.001 TYR C 143 PHE 0.017 0.001 PHE N 55 TRP 0.013 0.001 TRP M 422 HIS 0.010 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00317 (28682) covalent geometry : angle 0.53292 (38852) SS BOND : bond 0.00765 ( 1) SS BOND : angle 2.39340 ( 2) hydrogen bonds : bond 0.04155 ( 1163) hydrogen bonds : angle 4.80899 ( 3219) metal coordination : bond 0.04883 ( 36) metal coordination : angle 9.17499 ( 81) Misc. bond : bond 0.00098 ( 3) *********************** 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 458 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 393 time to evaluate : 0.973 Fit side-chains REVERT: A 292 MET cc_start: 0.8186 (tpt) cc_final: 0.7762 (tpt) REVERT: A 333 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: A 455 LEU cc_start: 0.8097 (mp) cc_final: 0.7831 (tm) REVERT: E 69 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8075 (pttm) REVERT: E 111 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: F 25 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: G 84 LEU cc_start: 0.8401 (mm) cc_final: 0.8113 (mm) REVERT: H 60 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7975 (mtmt) REVERT: I 93 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8376 (mptp) REVERT: J 286 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6630 (mmt180) REVERT: L 69 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: L 149 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: M 98 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8356 (ttpp) REVERT: N 25 ARG cc_start: 0.7788 (ttt180) cc_final: 0.6603 (ttm170) REVERT: N 101 LYS cc_start: 0.7928 (ptpp) cc_final: 0.7626 (ptmt) REVERT: O 56 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6687 (p) REVERT: O 103 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7876 (pt0) REVERT: O 166 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7302 (p0) REVERT: P 63 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: P 144 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9109 (mttt) REVERT: Q 205 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: T 64 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7737 (mp0) outliers start: 65 outliers final: 37 residues processed: 433 average time/residue: 0.7910 time to fit residues: 388.9135 Evaluate side-chains 435 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 48 optimal weight: 0.0070 chunk 248 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN C 123 GLN E 51 GLN H 71 GLN I 9 GLN K 79 HIS M 540 ASN N 52 ASN T 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102800 restraints weight = 32913.971| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.21 r_work: 0.2957 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.176 28722 Z= 0.103 Angle : 0.675 45.711 38935 Z= 0.262 Chirality : 0.042 0.168 4220 Planarity : 0.004 0.054 4998 Dihedral : 8.693 175.779 4087 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.94 % Allowed : 13.86 % Favored : 84.21 % 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: 0.77 (0.14), residues: 3439 helix: 1.50 (0.14), residues: 1340 sheet: 0.01 (0.26), residues: 387 loop : -0.09 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 538 TYR 0.014 0.001 TYR J 180 PHE 0.015 0.001 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.010 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00226 (28682) covalent geometry : angle 0.49760 (38852) SS BOND : bond 0.00607 ( 1) SS BOND : angle 2.25470 ( 2) hydrogen bonds : bond 0.03538 ( 1163) hydrogen bonds : angle 4.68362 ( 3219) metal coordination : bond 0.03084 ( 36) metal coordination : angle 9.99763 ( 81) Misc. bond : bond 0.00071 ( 3) *********************** 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 458 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 1.124 Fit side-chains REVERT: A 292 MET cc_start: 0.8187 (tpt) cc_final: 0.7757 (tpt) REVERT: A 333 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: A 455 LEU cc_start: 0.8089 (mp) cc_final: 0.7826 (tm) REVERT: E 69 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8123 (pttm) REVERT: E 111 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: F 25 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 92 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: G 84 LEU cc_start: 0.8364 (mm) cc_final: 0.8057 (mm) REVERT: H 60 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7919 (mtmt) REVERT: I 93 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8323 (mptp) REVERT: J 286 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6545 (mmt180) REVERT: L 69 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: L 149 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: M 98 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: N 25 ARG cc_start: 0.7697 (ttt180) cc_final: 0.6492 (ttm170) REVERT: N 101 LYS cc_start: 0.7846 (ptpp) cc_final: 0.7541 (ptmt) REVERT: O 56 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6509 (p) REVERT: O 103 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7820 (pt0) REVERT: O 166 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7268 (p0) REVERT: P 63 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: P 144 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8753 (mtmt) REVERT: Q 205 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: T 64 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 58 outliers final: 28 residues processed: 433 average time/residue: 0.7726 time to fit residues: 381.8027 Evaluate side-chains 425 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 380 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN F 76 ASN H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102295 restraints weight = 32737.330| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.20 r_work: 0.2925 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.254 28722 Z= 0.128 Angle : 0.677 40.218 38935 Z= 0.276 Chirality : 0.043 0.176 4220 Planarity : 0.005 0.054 4998 Dihedral : 8.757 179.443 4087 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.97 % Allowed : 14.09 % Favored : 83.94 % 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: 0.73 (0.14), residues: 3439 helix: 1.44 (0.14), residues: 1339 sheet: 0.04 (0.26), residues: 387 loop : -0.10 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 269 TYR 0.016 0.001 TYR C 143 PHE 0.016 0.001 PHE N 55 TRP 0.013 0.001 TRP M 422 HIS 0.011 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00291 (28682) covalent geometry : angle 0.52787 (38852) SS BOND : bond 0.00709 ( 1) SS BOND : angle 2.30152 ( 2) hydrogen bonds : bond 0.03976 ( 1163) hydrogen bonds : angle 4.73905 ( 3219) metal coordination : bond 0.04397 ( 36) metal coordination : angle 9.28846 ( 81) Misc. bond : bond 0.00096 ( 3) *********************** 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 443 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 0.976 Fit side-chains REVERT: A 292 MET cc_start: 0.8168 (tpt) cc_final: 0.7723 (tpt) REVERT: A 333 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: A 455 LEU cc_start: 0.8106 (mp) cc_final: 0.7851 (tm) REVERT: E 69 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8151 (pttm) REVERT: E 111 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: F 25 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: G 84 LEU cc_start: 0.8444 (mm) cc_final: 0.8147 (mm) REVERT: H 60 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: I 93 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8380 (mptp) REVERT: J 286 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6643 (mmt180) REVERT: L 69 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: L 112 MET cc_start: 0.8036 (mmm) cc_final: 0.7728 (mmp) REVERT: L 149 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: M 98 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8357 (ttpp) REVERT: N 25 ARG cc_start: 0.7778 (ttt180) cc_final: 0.6594 (ttm170) REVERT: N 101 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7614 (ptmt) REVERT: O 56 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6653 (p) REVERT: O 103 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7827 (pt0) REVERT: O 166 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7274 (p0) REVERT: P 63 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: P 144 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8787 (mtmt) REVERT: Q 205 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: T 64 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: T 119 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7442 (ttp80) outliers start: 59 outliers final: 33 residues processed: 422 average time/residue: 0.7850 time to fit residues: 377.5083 Evaluate side-chains 430 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 380 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 119 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 58 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 312 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN C 123 GLN F 76 ASN H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN P 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096391 restraints weight = 32627.944| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.33 r_work: 0.2877 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.395 28722 Z= 0.206 Angle : 0.741 35.475 38935 Z= 0.325 Chirality : 0.047 0.189 4220 Planarity : 0.005 0.055 4998 Dihedral : 9.074 171.338 4087 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.90 % Allowed : 14.02 % Favored : 84.07 % 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: 0.47 (0.14), residues: 3439 helix: 1.15 (0.14), residues: 1337 sheet: 0.19 (0.26), residues: 371 loop : -0.26 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 269 TYR 0.023 0.002 TYR C 143 PHE 0.023 0.002 PHE N 55 TRP 0.013 0.002 TRP M 510 HIS 0.014 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00487 (28682) covalent geometry : angle 0.61987 (38852) SS BOND : bond 0.00963 ( 1) SS BOND : angle 2.48200 ( 2) hydrogen bonds : bond 0.05179 ( 1163) hydrogen bonds : angle 5.05688 ( 3219) metal coordination : bond 0.06785 ( 36) metal coordination : angle 8.91723 ( 81) Misc. bond : bond 0.00162 ( 3) ********************** 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 451 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 394 time to evaluate : 1.170 Fit side-chains REVERT: A 333 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: A 455 LEU cc_start: 0.8118 (mp) cc_final: 0.7822 (tm) REVERT: E 69 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7990 (pttm) REVERT: E 111 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: F 25 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: G 84 LEU cc_start: 0.8387 (mm) cc_final: 0.8094 (mm) REVERT: H 60 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7957 (mtmt) REVERT: H 73 GLN cc_start: 0.8361 (mm110) cc_final: 0.8136 (mt0) REVERT: J 286 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6658 (mmt180) REVERT: J 322 VAL cc_start: 0.8500 (m) cc_final: 0.8246 (p) REVERT: L 69 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: L 149 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: M 98 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8430 (ttpp) REVERT: N 25 ARG cc_start: 0.7806 (ttt180) cc_final: 0.6550 (ttm170) REVERT: N 101 LYS cc_start: 0.7983 (ptpp) cc_final: 0.7681 (ptmt) REVERT: O 56 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6807 (p) REVERT: O 103 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7817 (pt0) REVERT: O 166 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7208 (p0) REVERT: P 63 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: Q 205 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: T 64 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: T 119 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7465 (ttp80) REVERT: W 27 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7136 (ttp80) outliers start: 57 outliers final: 35 residues processed: 429 average time/residue: 0.8060 time to fit residues: 393.6094 Evaluate side-chains 430 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 380 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 286 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 119 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 260 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 221 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 chunk 338 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN C 123 GLN F 76 ASN H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN N 52 ASN P 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.099304 restraints weight = 32915.509| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.22 r_work: 0.2905 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.245 28722 Z= 0.132 Angle : 0.702 44.412 38935 Z= 0.285 Chirality : 0.043 0.177 4220 Planarity : 0.005 0.056 4998 Dihedral : 8.881 174.839 4087 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 14.39 % Favored : 83.71 % 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: 0.55 (0.14), residues: 3439 helix: 1.27 (0.14), residues: 1335 sheet: -0.03 (0.26), residues: 387 loop : -0.19 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 538 TYR 0.016 0.001 TYR J 180 PHE 0.017 0.001 PHE N 55 TRP 0.013 0.001 TRP M 422 HIS 0.011 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00303 (28682) covalent geometry : angle 0.54176 (38852) SS BOND : bond 0.00728 ( 1) SS BOND : angle 2.37996 ( 2) hydrogen bonds : bond 0.04151 ( 1163) hydrogen bonds : angle 4.87868 ( 3219) metal coordination : bond 0.04267 ( 36) metal coordination : angle 9.79678 ( 81) Misc. bond : bond 0.00102 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11941.66 seconds wall clock time: 203 minutes 32.93 seconds (12212.93 seconds total)