Starting phenix.real_space_refine on Sat Feb 7 01:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vy8_32196/02_2026/7vy8_32196.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vy8_32196/02_2026/7vy8_32196.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/7vy8_32196/02_2026/7vy8_32196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vy8_32196/02_2026/7vy8_32196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vy8_32196/02_2026/7vy8_32196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vy8_32196/02_2026/7vy8_32196.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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18081 2.51 5 N 4960 2.21 5 O 5256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28527 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.312 49.216 107.689 1.00 14.92 S ATOM 3060 SG CYS A 425 46.786 46.023 113.585 1.00 19.73 S ATOM 2738 SG CYS A 385 44.161 44.677 107.956 1.00 17.97 S ATOM 2699 SG CYS A 379 42.067 49.723 111.715 1.00 18.05 S ATOM 3961 SG CYS B 113 34.949 63.208 72.674 1.00 6.02 S ATOM 3980 SG CYS B 116 40.306 61.231 76.393 1.00 14.29 S ATOM 4003 SG CYS B 119 41.072 63.709 70.760 1.00 18.24 S ATOM 4332 SG CYS B 162 38.664 57.899 71.746 1.00 9.85 S ATOM 4030 SG CYS B 123 46.900 66.518 65.905 1.00 9.07 S ATOM 4256 SG CYS B 152 45.041 64.452 60.155 1.00 12.92 S ATOM 4303 SG CYS B 158 43.328 60.908 65.363 1.00 17.63 S ATOM 4282 SG CYS B 155 49.309 61.230 63.513 1.00 13.19 S ATOM 5724 SG CYS C 166 51.581 64.482 55.813 1.00 15.46 S ATOM 4996 SG CYS C 72 51.759 65.648 49.485 1.00 14.44 S ATOM 4990 SG CYS C 71 57.254 64.307 52.404 1.00 12.45 S ATOM 5494 SG CYS C 136 53.709 69.507 54.477 1.00 14.43 S ATOM 14949 SG CYS M 131 39.631 61.770 88.414 1.00 17.69 S ATOM 14928 SG CYS M 128 43.272 57.118 85.419 1.00 21.20 S ATOM 14989 SG CYS M 137 45.344 60.869 90.501 1.00 4.24 S ATOM 15321 SG CYS M 179 44.072 61.286 101.501 1.00 10.01 S ATOM 15675 SG CYS M 226 40.785 63.753 97.233 1.00 20.08 S ATOM 15345 SG CYS M 182 38.578 64.027 103.294 1.00 23.47 S ATOM 15298 SG CYS M 176 38.424 58.328 100.159 1.00 11.39 S ATOM 14546 SG CYS M 78 55.718 57.089 105.167 1.00 24.88 S ATOM 14647 SG CYS M 92 53.889 59.237 107.420 1.00 24.18 S ATOM 14435 SG CYS M 64 49.507 59.079 105.336 1.00 6.30 S ATOM 14521 SG CYS M 75 50.579 57.033 102.280 1.00 12.03 S ATOM 21484 SG CYS O 135 31.941 31.680 116.737 1.00 32.00 S ATOM 21518 SG CYS O 140 31.884 28.238 117.984 1.00 42.14 S ATOM 21798 SG CYS O 176 36.345 33.337 119.368 1.00 49.30 S ATOM 21821 SG CYS O 180 36.802 30.038 120.157 1.00 43.28 S ATOM 27631 SG CYS T 86 27.992 50.210 81.212 1.00 17.83 S ATOM 27809 SG CYS T 111 29.217 53.711 81.846 1.00 32.80 S Time building chain proxies: 5.49, per 1000 atoms: 0.19 Number of scatterers: 28527 At special positions: 0 Unit cell: (123.533, 140.72, 164.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 11 15.00 Mg 1 11.99 O 5256 8.00 N 4960 7.00 C 18081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " 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="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " 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=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 31 sheets defined 45.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.871A pdb=" N GLY A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) 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 134 Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.704A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 203 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: 3.719A 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 261 through 264 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.606A pdb=" N GLU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 4.386A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 4.031A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 207 removed outlier: 5.627A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 70 through 80 removed outlier: 3.990A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 removed outlier: 3.504A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 removed outlier: 3.519A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.536A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 40 through 48 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.704A 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: 3.708A 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 58 through 62 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.548A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 5.302A 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: 3.553A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 220 removed outlier: 3.662A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 224 Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.942A pdb=" N LYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 315 through 323 Processing helix chain 'J' and resid 334 through 339 removed outlier: 3.515A pdb=" N GLY J 339 " --> pdb=" O GLU J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 349 through 354 Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.956A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.562A pdb=" N THR L 65 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 74 Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.561A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.436A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'M' and resid 133 through 136 Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.742A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET M 204 " --> pdb=" O GLY M 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 200 through 204' Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.996A 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: 3.733A pdb=" N ARG M 299 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.526A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE M 333 " --> pdb=" O MET M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 removed outlier: 3.642A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.767A 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: 3.938A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 4.295A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 483 Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 3.561A pdb=" N ARG M 655 " --> pdb=" O ASN M 652 " (cutoff:3.500A) Processing helix chain 'M' and resid 664 through 673 Processing helix chain 'M' and resid 690 through 694 Processing helix chain 'M' and resid 698 through 704 Processing helix chain 'M' and resid 704 through 716 removed outlier: 3.544A pdb=" N ALA M 708 " --> pdb=" O SER M 704 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 31 removed outlier: 3.722A pdb=" N GLY N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 68 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.643A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.602A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 3.990A 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 209 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: 4.065A 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 88 through 92 removed outlier: 4.230A pdb=" N HIS Q 92 " --> pdb=" O PRO Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 125 Processing helix chain 'Q' and resid 132 through 140 removed outlier: 3.908A pdb=" N PHE Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.762A 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: 4.380A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 263 removed outlier: 3.565A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.607A pdb=" N VAL Q 314 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 372 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 434 removed outlier: 4.008A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 439 Processing helix chain 'Q' and resid 443 through 454 Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.571A 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: 6.320A pdb=" N ALA A 154 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 198 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE A 156 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.606A 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 removed outlier: 3.553A pdb=" N ARG A 267 " --> pdb=" O ASN A 270 " (cutoff:3.500A) 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 103 removed outlier: 4.159A pdb=" N GLU B 100 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.546A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 102 through 106 removed outlier: 7.023A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.475A 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 removed outlier: 8.619A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 67 through 71 removed outlier: 5.459A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.336A 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: 6.560A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.534A 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 226 through 228 removed outlier: 5.871A pdb=" N VAL J 226 " --> pdb=" O TYR J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB5, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB7, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.169A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AC1, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.804A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.852A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL M 338 " --> pdb=" O SER M 365 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.863A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 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: 5.570A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.831A 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: 6.704A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC9, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.330A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD2, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD3, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'T' and resid 83 through 86 1140 hydrogen bonds defined for protein. 3123 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: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11770 1.40 - 1.62: 17072 1.62 - 1.84: 281 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 29203 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.261 0.263 2.00e-02 2.50e+03 1.72e+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 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 29198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 39271 3.32 - 6.63: 234 6.63 - 9.95: 44 9.95 - 13.26: 20 13.26 - 16.58: 8 Bond angle restraints: 39577 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 107.74 124.25 -16.51 1.95e+00 2.62e-01 7.14e+01 angle pdb=" C HIS M 460 " pdb=" N PRO M 461 " pdb=" CA PRO M 461 " ideal model delta sigma weight residual 119.05 126.99 -7.94 1.11e+00 8.12e-01 5.11e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.41 8.05 1.17e+00 7.36e-01 4.77e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.93 -8.60 1.32e+00 5.72e-01 4.23e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 ... (remaining 39572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 16869 31.01 - 62.02: 764 62.02 - 93.03: 62 93.03 - 124.05: 5 124.05 - 155.06: 7 Dihedral angle restraints: 17707 sinusoidal: 7478 harmonic: 10229 Sorted by residual: dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" C2 PLX C 303 " pdb=" O1 PLX C 303 " pdb=" P1 PLX C 303 " pdb=" O3 PLX C 303 " ideal model delta sinusoidal sigma weight residual 310.56 155.50 155.06 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C2 PLX C 303 " pdb=" O1 PLX C 303 " pdb=" P1 PLX C 303 " pdb=" O2 PLX C 303 " ideal model delta sinusoidal sigma weight residual 178.46 36.16 142.30 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 17704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3807 0.071 - 0.143: 462 0.143 - 0.214: 7 0.214 - 0.286: 3 0.286 - 0.357: 4 Chirality restraints: 4283 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 3.19e+00 chirality pdb=" C6 PLX C 303 " pdb=" C7 PLX C 303 " pdb=" O6 PLX C 303 " pdb=" O7 PLX C 303 " both_signs ideal model delta sigma weight residual False 2.01 2.35 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA CYS A 187 " pdb=" N CYS A 187 " pdb=" C CYS A 187 " pdb=" CB CYS A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 4280 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " -0.334 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C13 UQ J 402 " 0.315 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.380 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.003 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.046 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C11 UQ J 402 " 0.006 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.306 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.571 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.081 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C3N NDP J 401 " 0.401 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.068 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.251 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.164 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 285 2.63 - 3.19: 24410 3.19 - 3.76: 45589 3.76 - 4.33: 67341 4.33 - 4.90: 106990 Nonbonded interactions: 244615 Sorted by model distance: nonbonded pdb=" N SER G 112 " pdb=" O1 8Q1 G 201 " model vdw 2.057 2.496 nonbonded pdb=" N1 FMN A 502 " pdb=" O3' FMN A 502 " model vdw 2.133 3.120 nonbonded pdb=" OG SER J 178 " pdb=" OD2 ASP J 317 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLU M 81 " pdb=" OG SER M 106 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN A 277 " pdb=" OG1 THR A 287 " model vdw 2.209 3.040 ... (remaining 244610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.380 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.317 29240 Z= 0.377 Angle : 0.837 18.729 39660 Z= 0.387 Chirality : 0.046 0.357 4283 Planarity : 0.010 0.311 5092 Dihedral : 16.725 155.058 11128 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 0.99 % Allowed : 13.15 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3502 helix: 0.95 (0.14), residues: 1332 sheet: 0.19 (0.26), residues: 376 loop : -0.42 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 96 TYR 0.023 0.002 TYR C 142 PHE 0.017 0.002 PHE Q 204 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00821 (29203) covalent geometry : angle 0.77515 (39577) SS BOND : bond 0.00876 ( 1) SS BOND : angle 2.60307 ( 2) hydrogen bonds : bond 0.15332 ( 1140) hydrogen bonds : angle 6.44137 ( 3123) metal coordination : bond 0.01097 ( 35) metal coordination : angle 7.03125 ( 81) Misc. bond : bond 0.10525 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 384 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: O 245 VAL cc_start: 0.8985 (p) cc_final: 0.8692 (t) outliers start: 30 outliers final: 22 residues processed: 405 average time/residue: 0.7985 time to fit residues: 367.1498 Evaluate side-chains 397 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 375 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 212 GLU Chi-restraints excluded: chain Q residue 217 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN F 31 GLN H 73 GLN I 21 GLN I 29 GLN I 51 ASN J 341 GLN L 88 GLN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095874 restraints weight = 34953.662| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.16 r_work: 0.2913 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29240 Z= 0.124 Angle : 0.629 20.904 39660 Z= 0.282 Chirality : 0.043 0.151 4283 Planarity : 0.005 0.077 5092 Dihedral : 10.549 145.750 4200 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.84 % Allowed : 12.69 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3502 helix: 1.35 (0.14), residues: 1346 sheet: 0.11 (0.26), residues: 378 loop : -0.32 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.019 0.001 TYR Q 308 PHE 0.016 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00276 (29203) covalent geometry : angle 0.53968 (39577) SS BOND : bond 0.00481 ( 1) SS BOND : angle 2.45602 ( 2) hydrogen bonds : bond 0.04452 ( 1140) hydrogen bonds : angle 5.04902 ( 3123) metal coordination : bond 0.00961 ( 35) metal coordination : angle 7.17035 ( 81) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 392 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: G 87 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7906 (mp) REVERT: I 70 MET cc_start: 0.7462 (tmt) cc_final: 0.6891 (tmt) REVERT: J 234 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: M 108 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8430 (ttmm) REVERT: M 468 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7322 (mm-30) REVERT: O 245 VAL cc_start: 0.8944 (p) cc_final: 0.8628 (t) REVERT: P 225 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: Q 222 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8503 (mtp) outliers start: 56 outliers final: 27 residues processed: 427 average time/residue: 0.8838 time to fit residues: 428.8297 Evaluate side-chains 403 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 210 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 342 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 21 GLN I 29 GLN I 51 ASN J 341 GLN L 88 GLN M 30 ASN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 55 HIS P 63 GLN P 82 ASN P 123 GLN T 122 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.094101 restraints weight = 34939.407| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.16 r_work: 0.2887 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29240 Z= 0.160 Angle : 0.641 20.182 39660 Z= 0.290 Chirality : 0.044 0.159 4283 Planarity : 0.005 0.065 5092 Dihedral : 9.822 158.974 4176 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 2.70 % Allowed : 12.56 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3502 helix: 1.36 (0.14), residues: 1346 sheet: 0.21 (0.27), residues: 353 loop : -0.39 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.019 0.002 TYR J 180 PHE 0.016 0.002 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00380 (29203) covalent geometry : angle 0.55247 (39577) SS BOND : bond 0.00528 ( 1) SS BOND : angle 2.80395 ( 2) hydrogen bonds : bond 0.04718 ( 1140) hydrogen bonds : angle 4.93080 ( 3123) metal coordination : bond 0.01289 ( 35) metal coordination : angle 7.18912 ( 81) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 383 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8738 (pp) REVERT: E 92 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: F 46 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7651 (mmtp) REVERT: I 70 MET cc_start: 0.7618 (tmt) cc_final: 0.7409 (tmt) REVERT: J 234 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: J 299 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7665 (mtp85) REVERT: M 108 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: M 468 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7420 (mm-30) REVERT: N 41 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: O 245 VAL cc_start: 0.8952 (p) cc_final: 0.8640 (t) REVERT: P 225 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: Q 222 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8508 (mtp) REVERT: Q 281 GLU cc_start: 0.8679 (tp30) cc_final: 0.8233 (mp0) REVERT: Q 308 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.6026 (p90) REVERT: T 46 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7904 (m-30) outliers start: 82 outliers final: 45 residues processed: 426 average time/residue: 0.8553 time to fit residues: 415.5936 Evaluate side-chains 421 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 367 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 100 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 21 GLN I 29 GLN I 51 ASN J 341 GLN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095883 restraints weight = 34802.602| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.16 r_work: 0.2924 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29240 Z= 0.110 Angle : 0.594 21.433 39660 Z= 0.264 Chirality : 0.042 0.150 4283 Planarity : 0.004 0.059 5092 Dihedral : 9.303 165.941 4175 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 2.14 % Allowed : 13.58 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3502 helix: 1.51 (0.15), residues: 1346 sheet: 0.00 (0.25), residues: 379 loop : -0.28 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.016 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00248 (29203) covalent geometry : angle 0.50233 (39577) SS BOND : bond 0.00585 ( 1) SS BOND : angle 2.50309 ( 2) hydrogen bonds : bond 0.03912 ( 1140) hydrogen bonds : angle 4.73629 ( 3123) metal coordination : bond 0.00866 ( 35) metal coordination : angle 7.01932 ( 81) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8731 (pp) REVERT: C 51 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8317 (t0) REVERT: H 105 GLU cc_start: 0.8260 (tp30) cc_final: 0.8008 (tp30) REVERT: I 70 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7354 (tmt) REVERT: J 234 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: J 299 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7690 (mtp85) REVERT: M 108 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: M 468 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7468 (mm-30) REVERT: O 245 VAL cc_start: 0.9019 (p) cc_final: 0.8712 (t) REVERT: P 56 LYS cc_start: 0.8922 (mttt) cc_final: 0.8498 (mmpt) REVERT: P 225 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: Q 222 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8455 (mtp) REVERT: Q 281 GLU cc_start: 0.8666 (tp30) cc_final: 0.8235 (mp0) REVERT: Q 308 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.5838 (p90) outliers start: 65 outliers final: 35 residues processed: 430 average time/residue: 0.8577 time to fit residues: 420.6661 Evaluate side-chains 417 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 154 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN H 41 ASN I 21 GLN I 29 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 514 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095507 restraints weight = 34883.164| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.16 r_work: 0.2899 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29240 Z= 0.135 Angle : 0.611 20.549 39660 Z= 0.273 Chirality : 0.043 0.149 4283 Planarity : 0.005 0.059 5092 Dihedral : 9.129 164.642 4175 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 2.47 % Allowed : 13.78 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3502 helix: 1.51 (0.15), residues: 1345 sheet: 0.02 (0.26), residues: 360 loop : -0.31 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.018 0.001 TYR J 180 PHE 0.016 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00317 (29203) covalent geometry : angle 0.52176 (39577) SS BOND : bond 0.00526 ( 1) SS BOND : angle 2.65550 ( 2) hydrogen bonds : bond 0.04180 ( 1140) hydrogen bonds : angle 4.72976 ( 3123) metal coordination : bond 0.01079 ( 35) metal coordination : angle 7.03683 ( 81) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 383 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8729 (pp) REVERT: C 51 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 92 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: F 17 ARG cc_start: 0.9321 (mmt-90) cc_final: 0.8963 (mmt180) REVERT: F 46 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7729 (mmtp) REVERT: H 105 GLU cc_start: 0.8269 (tp30) cc_final: 0.8025 (tp30) REVERT: I 33 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8588 (mmtm) REVERT: I 70 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7410 (tmt) REVERT: J 234 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: J 303 ARG cc_start: 0.7884 (tpt170) cc_final: 0.7644 (tpt170) REVERT: M 98 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7935 (tptt) REVERT: M 108 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8411 (ttmm) REVERT: M 468 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7604 (mm-30) REVERT: N 41 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: O 245 VAL cc_start: 0.9015 (p) cc_final: 0.8721 (t) REVERT: P 56 LYS cc_start: 0.8933 (mttt) cc_final: 0.8503 (mmpt) REVERT: P 225 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: Q 222 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: Q 281 GLU cc_start: 0.8676 (tp30) cc_final: 0.8214 (mp0) REVERT: Q 292 MET cc_start: 0.9368 (mmm) cc_final: 0.9077 (mmm) REVERT: Q 308 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.5981 (p90) outliers start: 75 outliers final: 41 residues processed: 427 average time/residue: 0.8720 time to fit residues: 422.5695 Evaluate side-chains 426 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 79 optimal weight: 0.6980 chunk 276 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 319 optimal weight: 0.0170 chunk 114 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 21 GLN I 29 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095377 restraints weight = 34913.102| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.16 r_work: 0.2904 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29240 Z= 0.130 Angle : 0.605 20.779 39660 Z= 0.271 Chirality : 0.043 0.149 4283 Planarity : 0.004 0.061 5092 Dihedral : 8.939 159.112 4175 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 2.56 % Allowed : 13.84 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3502 helix: 1.53 (0.14), residues: 1345 sheet: 0.00 (0.26), residues: 360 loop : -0.30 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 269 TYR 0.017 0.001 TYR J 180 PHE 0.016 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00303 (29203) covalent geometry : angle 0.51603 (39577) SS BOND : bond 0.00556 ( 1) SS BOND : angle 2.67005 ( 2) hydrogen bonds : bond 0.04092 ( 1140) hydrogen bonds : angle 4.69898 ( 3123) metal coordination : bond 0.01021 ( 35) metal coordination : angle 6.98270 ( 81) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 114 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8731 (pp) REVERT: F 17 ARG cc_start: 0.9334 (mmt-90) cc_final: 0.8962 (mmt180) REVERT: H 105 GLU cc_start: 0.8213 (tp30) cc_final: 0.7981 (tp30) REVERT: I 33 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8592 (mmtm) REVERT: I 70 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7205 (tmt) REVERT: J 234 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: J 303 ARG cc_start: 0.7886 (tpt170) cc_final: 0.7637 (tpt170) REVERT: M 98 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7932 (tptt) REVERT: M 108 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8392 (ttmm) REVERT: O 245 VAL cc_start: 0.9058 (p) cc_final: 0.8766 (t) REVERT: P 56 LYS cc_start: 0.8923 (mttt) cc_final: 0.8501 (mmpt) REVERT: P 225 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: Q 222 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8407 (mtp) REVERT: Q 281 GLU cc_start: 0.8677 (tp30) cc_final: 0.8220 (mp0) REVERT: Q 292 MET cc_start: 0.9354 (mmm) cc_final: 0.8996 (mmm) REVERT: Q 308 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.5894 (p90) outliers start: 78 outliers final: 44 residues processed: 435 average time/residue: 0.8560 time to fit residues: 423.2589 Evaluate side-chains 427 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 373 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 230 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 90 optimal weight: 0.0020 chunk 116 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN H 41 ASN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN O 131 HIS P 63 GLN P 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.091129 restraints weight = 34838.465| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.19 r_work: 0.2838 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29240 Z= 0.266 Angle : 0.723 18.632 39660 Z= 0.338 Chirality : 0.049 0.168 4283 Planarity : 0.006 0.061 5092 Dihedral : 9.353 152.222 4175 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 2.86 % Allowed : 13.71 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3502 helix: 1.18 (0.14), residues: 1348 sheet: -0.08 (0.26), residues: 367 loop : -0.47 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 96 TYR 0.024 0.002 TYR J 180 PHE 0.021 0.002 PHE J 195 TRP 0.015 0.002 TRP M 510 HIS 0.009 0.002 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00647 (29203) covalent geometry : angle 0.64424 (39577) SS BOND : bond 0.00471 ( 1) SS BOND : angle 3.33311 ( 2) hydrogen bonds : bond 0.05620 ( 1140) hydrogen bonds : angle 5.04163 ( 3123) metal coordination : bond 0.01853 ( 35) metal coordination : angle 7.27843 ( 81) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 114 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8872 (pp) REVERT: E 92 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: F 17 ARG cc_start: 0.9357 (mmt-90) cc_final: 0.9004 (mmt180) REVERT: H 105 GLU cc_start: 0.8288 (tp30) cc_final: 0.8038 (tp30) REVERT: I 33 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8554 (mmtm) REVERT: I 70 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7600 (tmt) REVERT: J 234 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: M 98 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8031 (tptt) REVERT: M 108 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8506 (ttmm) REVERT: N 41 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: N 54 GLN cc_start: 0.8238 (mp10) cc_final: 0.8009 (mp10) REVERT: N 95 ASP cc_start: 0.8892 (m-30) cc_final: 0.8638 (m-30) REVERT: O 245 VAL cc_start: 0.9057 (p) cc_final: 0.8750 (t) REVERT: P 225 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: Q 222 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8610 (mtp) REVERT: Q 281 GLU cc_start: 0.8691 (tp30) cc_final: 0.8206 (mp0) REVERT: Q 292 MET cc_start: 0.9379 (mmm) cc_final: 0.9134 (mmm) REVERT: Q 308 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.6139 (p90) outliers start: 87 outliers final: 49 residues processed: 436 average time/residue: 0.7850 time to fit residues: 389.1196 Evaluate side-chains 430 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 269 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 182 optimal weight: 0.6980 chunk 285 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN H 41 ASN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.095720 restraints weight = 34936.788| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.15 r_work: 0.2908 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29240 Z= 0.118 Angle : 0.606 21.358 39660 Z= 0.272 Chirality : 0.042 0.149 4283 Planarity : 0.005 0.062 5092 Dihedral : 8.761 135.470 4175 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.20 % Allowed : 14.37 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3502 helix: 1.44 (0.14), residues: 1346 sheet: -0.00 (0.26), residues: 349 loop : -0.35 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 96 TYR 0.017 0.001 TYR J 180 PHE 0.016 0.001 PHE Q 458 TRP 0.014 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00267 (29203) covalent geometry : angle 0.51727 (39577) SS BOND : bond 0.00586 ( 1) SS BOND : angle 2.62131 ( 2) hydrogen bonds : bond 0.03974 ( 1140) hydrogen bonds : angle 4.72647 ( 3123) metal coordination : bond 0.00949 ( 35) metal coordination : angle 6.97349 ( 81) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8733 (pp) REVERT: F 17 ARG cc_start: 0.9338 (mmt-90) cc_final: 0.9001 (mmt180) REVERT: F 46 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7641 (mmtp) REVERT: I 33 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8604 (mmtm) REVERT: J 234 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: J 303 ARG cc_start: 0.7910 (tpt170) cc_final: 0.7524 (tpt170) REVERT: L 86 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8363 (t0) REVERT: M 108 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8366 (ttmm) REVERT: N 51 ASP cc_start: 0.8369 (t70) cc_final: 0.7982 (t0) REVERT: O 245 VAL cc_start: 0.9052 (p) cc_final: 0.8748 (t) REVERT: P 127 GLU cc_start: 0.8644 (tt0) cc_final: 0.8439 (tt0) REVERT: P 225 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: Q 281 GLU cc_start: 0.8674 (tp30) cc_final: 0.8223 (mp0) REVERT: Q 292 MET cc_start: 0.9347 (mmm) cc_final: 0.9078 (mmm) REVERT: Q 308 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.5955 (p90) outliers start: 67 outliers final: 40 residues processed: 422 average time/residue: 0.8038 time to fit residues: 385.0904 Evaluate side-chains 413 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 366 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 116 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 290 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 21 GLN I 51 ASN J 154 GLN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094890 restraints weight = 34807.260| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.15 r_work: 0.2890 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29240 Z= 0.145 Angle : 0.628 20.589 39660 Z= 0.283 Chirality : 0.043 0.148 4283 Planarity : 0.005 0.061 5092 Dihedral : 8.665 133.711 4175 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 14.76 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3502 helix: 1.45 (0.14), residues: 1345 sheet: -0.00 (0.26), residues: 356 loop : -0.35 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 52 TYR 0.018 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00343 (29203) covalent geometry : angle 0.54108 (39577) SS BOND : bond 0.00538 ( 1) SS BOND : angle 2.72255 ( 2) hydrogen bonds : bond 0.04292 ( 1140) hydrogen bonds : angle 4.74914 ( 3123) metal coordination : bond 0.01121 ( 35) metal coordination : angle 7.04652 ( 81) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 373 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8751 (pp) REVERT: E 116 THR cc_start: 0.8849 (p) cc_final: 0.8581 (t) REVERT: F 17 ARG cc_start: 0.9343 (mmt-90) cc_final: 0.9000 (mmt180) REVERT: F 46 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7715 (mmtp) REVERT: I 33 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8550 (mmtm) REVERT: J 234 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: L 86 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8357 (t0) REVERT: M 108 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: N 51 ASP cc_start: 0.8289 (t70) cc_final: 0.7975 (t0) REVERT: O 245 VAL cc_start: 0.9033 (p) cc_final: 0.8737 (t) REVERT: P 127 GLU cc_start: 0.8663 (tt0) cc_final: 0.8437 (tt0) REVERT: P 225 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: Q 281 GLU cc_start: 0.8673 (tp30) cc_final: 0.8230 (mp0) REVERT: Q 292 MET cc_start: 0.9348 (mmm) cc_final: 0.9062 (mmm) REVERT: Q 308 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.5925 (p90) outliers start: 59 outliers final: 43 residues processed: 414 average time/residue: 0.7912 time to fit residues: 372.6015 Evaluate side-chains 415 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 365 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 160 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 44 optimal weight: 0.0170 chunk 293 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 21 GLN I 51 ASN J 154 GLN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094559 restraints weight = 34783.304| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.15 r_work: 0.2902 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29240 Z= 0.141 Angle : 0.627 20.697 39660 Z= 0.283 Chirality : 0.043 0.149 4283 Planarity : 0.005 0.061 5092 Dihedral : 8.533 131.794 4175 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 14.96 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3502 helix: 1.45 (0.14), residues: 1346 sheet: 0.02 (0.26), residues: 356 loop : -0.34 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.018 0.001 TYR J 180 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00334 (29203) covalent geometry : angle 0.54058 (39577) SS BOND : bond 0.00542 ( 1) SS BOND : angle 2.73471 ( 2) hydrogen bonds : bond 0.04253 ( 1140) hydrogen bonds : angle 4.72589 ( 3123) metal coordination : bond 0.01091 ( 35) metal coordination : angle 7.03859 ( 81) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8755 (pp) REVERT: E 116 THR cc_start: 0.8863 (p) cc_final: 0.8595 (t) REVERT: F 17 ARG cc_start: 0.9339 (mmt-90) cc_final: 0.9000 (mmt180) REVERT: F 46 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7731 (mmtp) REVERT: I 33 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8552 (mmtm) REVERT: J 234 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: L 86 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8344 (t0) REVERT: M 108 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8411 (ttmm) REVERT: N 51 ASP cc_start: 0.8293 (t70) cc_final: 0.8054 (t0) REVERT: O 245 VAL cc_start: 0.9045 (p) cc_final: 0.8755 (t) REVERT: P 127 GLU cc_start: 0.8648 (tt0) cc_final: 0.8423 (tt0) REVERT: P 225 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: Q 281 GLU cc_start: 0.8677 (tp30) cc_final: 0.8241 (mp0) REVERT: Q 292 MET cc_start: 0.9355 (mmm) cc_final: 0.9066 (mmm) REVERT: Q 308 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6031 (p90) outliers start: 55 outliers final: 46 residues processed: 411 average time/residue: 0.8814 time to fit residues: 411.9518 Evaluate side-chains 418 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 46 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 237 optimal weight: 0.0060 chunk 119 optimal weight: 0.9980 chunk 275 optimal weight: 0.0770 chunk 337 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 276 optimal weight: 0.0020 chunk 230 optimal weight: 0.0670 chunk 49 optimal weight: 0.7980 overall best weight: 0.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 51 ASN J 341 GLN M 123 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN P 63 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096181 restraints weight = 34910.738| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.23 r_work: 0.2954 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 29240 Z= 0.092 Angle : 0.585 22.416 39660 Z= 0.256 Chirality : 0.041 0.151 4283 Planarity : 0.004 0.062 5092 Dihedral : 8.035 121.855 4175 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.48 % Allowed : 15.59 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3502 helix: 1.65 (0.15), residues: 1351 sheet: -0.05 (0.25), residues: 382 loop : -0.20 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 269 TYR 0.015 0.001 TYR P 64 PHE 0.013 0.001 PHE Q 458 TRP 0.017 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00198 (29203) covalent geometry : angle 0.49613 (39577) SS BOND : bond 0.00549 ( 1) SS BOND : angle 2.14437 ( 2) hydrogen bonds : bond 0.03148 ( 1140) hydrogen bonds : angle 4.47878 ( 3123) metal coordination : bond 0.00756 ( 35) metal coordination : angle 6.85413 ( 81) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11467.83 seconds wall clock time: 195 minutes 49.65 seconds (11749.65 seconds total)