Starting phenix.real_space_refine on Sun Jul 5 14:42:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyh_32205/07_2026/7vyh_32205.map" } resolution = 2.9 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 9 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17680 2.51 5 N 4878 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27933 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1244 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 664 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2352 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5293 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "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: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1660 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 47.918 49.817 102.264 1.00 15.39 S ATOM 3048 SG CYS A 425 47.475 46.123 107.890 1.00 17.89 S ATOM 2726 SG CYS A 385 45.014 45.381 102.074 1.00 16.70 S ATOM 2687 SG CYS A 379 42.766 49.994 106.345 1.00 18.68 S ATOM 3949 SG CYS B 113 36.566 67.682 68.531 1.00 15.89 S ATOM 3968 SG CYS B 116 41.738 65.037 72.122 1.00 13.87 S ATOM 3991 SG CYS B 119 42.650 68.149 66.793 1.00 14.80 S ATOM 4320 SG CYS B 162 40.084 62.302 67.163 1.00 16.01 S ATOM 4018 SG CYS B 123 48.699 71.101 62.393 1.00 17.99 S ATOM 4244 SG CYS B 152 46.861 69.736 56.340 1.00 29.22 S ATOM 4291 SG CYS B 158 44.997 65.737 61.070 1.00 20.09 S ATOM 4270 SG CYS B 155 51.020 66.078 59.445 1.00 20.38 S ATOM 5708 SG CYS C 166 53.149 69.881 52.250 1.00 15.87 S ATOM 4978 SG CYS C 71 57.610 69.925 48.044 1.00 17.83 S ATOM 4984 SG CYS C 72 54.339 71.925 46.327 1.00 16.77 S ATOM 4978 SG CYS C 71 57.610 69.925 48.044 1.00 17.83 S ATOM 5478 SG CYS C 136 55.786 74.667 50.972 1.00 13.76 S ATOM 14498 SG CYS M 131 40.929 64.456 84.222 1.00 15.24 S ATOM 14477 SG CYS M 128 44.580 60.154 80.883 1.00 16.12 S ATOM 14538 SG CYS M 137 46.670 63.332 86.228 1.00 12.15 S ATOM 14870 SG CYS M 179 45.237 62.530 97.250 1.00 14.17 S ATOM 15224 SG CYS M 226 42.136 65.579 93.131 1.00 13.01 S ATOM 14894 SG CYS M 182 39.766 65.314 99.226 1.00 16.42 S ATOM 14847 SG CYS M 176 39.515 60.063 95.529 1.00 14.48 S ATOM 14095 SG CYS M 78 56.761 57.865 100.577 1.00 13.83 S ATOM 14196 SG CYS M 92 54.939 59.853 103.003 1.00 15.97 S ATOM 13984 SG CYS M 64 50.607 59.789 100.946 1.00 12.52 S ATOM 14070 SG CYS M 75 51.553 58.007 97.752 1.00 14.53 S ATOM 21030 SG CYS O 135 31.847 32.143 109.384 1.00 35.44 S ATOM 21064 SG CYS O 140 31.873 28.631 110.102 1.00 38.82 S ATOM 21344 SG CYS O 176 36.306 33.712 112.065 1.00 36.80 S ATOM 21367 SG CYS O 180 36.632 30.230 112.222 1.00 40.30 S ATOM 27114 SG CYS T 86 29.163 53.897 75.799 1.00 20.31 S ATOM 27292 SG CYS T 111 30.585 57.091 76.925 1.00 22.53 S Time building chain proxies: 4.85, per 1000 atoms: 0.17 Number of scatterers: 27933 At special positions: 0 Unit cell: (124.607, 143.943, 157.907, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 9 15.00 Mg 1 11.99 O 5148 8.00 N 4878 7.00 C 17680 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: 2.45 Conformation dependent library (CDL) restraints added in 812.6 milliseconds 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="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 30 sheets defined 45.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.626A pdb=" N ARG A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.555A pdb=" N LYS A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 150 removed outlier: 4.179A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 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 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.710A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.986A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.211A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.557A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 209 removed outlier: 5.770A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.860A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.631A pdb=" N PHE C 89 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.821A pdb=" N SER C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.639A pdb=" N MET C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.884A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.580A 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 removed outlier: 3.737A pdb=" N ILE E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 48 removed outlier: 7.228A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 97 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.630A pdb=" N TYR G 90 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.567A pdb=" N GLU G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 37 removed outlier: 3.970A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 65 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.590A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.501A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 92 removed outlier: 3.682A pdb=" N THR J 91 " --> pdb=" O GLU J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 Proline residue: J 96 - end of helix No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 112 through 120 removed outlier: 4.127A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 316 through 324 Processing helix chain 'J' and resid 334 through 339 Processing helix chain 'J' and resid 344 through 354 removed outlier: 4.041A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.524A pdb=" N HIS K 79 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.584A pdb=" N THR L 65 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 74 removed outlier: 3.786A pdb=" N LYS L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR L 74 " --> pdb=" O GLU L 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 74' Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 159 through 164 Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.463A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.536A pdb=" N ARG M 184 " --> pdb=" O THR M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 removed outlier: 4.071A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.981A 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: 3.580A pdb=" N ARG M 299 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.678A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 removed outlier: 3.551A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 4.201A pdb=" N LEU M 381 " --> pdb=" O GLY M 378 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG M 382 " --> pdb=" O THR M 379 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER M 383 " --> pdb=" O ASP M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 removed outlier: 3.578A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 458 removed outlier: 3.778A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 4.083A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU M 468 " --> pdb=" O GLN M 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 483 removed outlier: 3.980A pdb=" N ARG M 483 " --> pdb=" O SER M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 528 removed outlier: 3.540A pdb=" N ALA M 525 " --> pdb=" O SER M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 654 removed outlier: 3.728A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 654' 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 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 19 through 31 removed outlier: 3.542A pdb=" N TYR N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.994A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 70 removed outlier: 3.987A pdb=" N TYR O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.756A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.989A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.323A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.778A pdb=" N HIS P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 3.869A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.728A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 133 through 140 removed outlier: 4.169A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.738A 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: 4.244A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.556A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.866A 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: 3.660A 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 374 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 4.170A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.750A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 55 removed outlier: 3.745A 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: 6.268A pdb=" N ALA A 154 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 198 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE A 156 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.779A 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 removed outlier: 6.277A pdb=" N LYS B 39 " --> pdb=" O ILE Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.512A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 67 removed outlier: 6.550A pdb=" N MET C 65 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 106 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE C 67 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 58 Processing sheet with id=AA9, first strand: chain 'I' and resid 67 through 69 removed outlier: 6.602A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.311A 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: 6.467A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.210A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.645A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.592A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.270A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'N' and resid 37 through 41 removed outlier: 7.019A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.877A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.679A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC8, first strand: chain 'Q' and resid 80 through 84 removed outlier: 7.144A pdb=" N ARG Q 96 " --> pdb=" O PRO Q 111 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL Q 98 " --> pdb=" O CYS Q 109 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS Q 109 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET Q 105 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD1, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD2, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD3, first strand: chain 'T' and resid 83 through 86 1107 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 2.92 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: 11498 1.40 - 1.62: 16719 1.62 - 1.85: 273 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 28570 Sorted by residual: bond pdb=" C2B NDP J 401 " pdb=" C3B NDP J 401 " ideal model delta sigma weight residual 1.552 1.238 0.314 3.50e-02 8.16e+02 8.03e+01 bond pdb=" C5N NDP J 401 " pdb=" C6N NDP J 401 " ideal model delta sigma weight residual 1.337 1.551 -0.214 2.40e-02 1.74e+03 7.96e+01 bond pdb=" CA7 CDL N 201 " pdb=" OA8 CDL N 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.59e+01 bond pdb=" C3D NDP J 401 " pdb=" C4D NDP J 401 " ideal model delta sigma weight residual 1.550 1.271 0.279 3.60e-02 7.72e+02 5.99e+01 bond pdb=" C2N NDP J 401 " pdb=" C3N NDP J 401 " ideal model delta sigma weight residual 1.357 1.550 -0.193 2.50e-02 1.60e+03 5.98e+01 ... (remaining 28565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 38413 3.32 - 6.64: 227 6.64 - 9.96: 35 9.96 - 13.28: 13 13.28 - 16.60: 6 Bond angle restraints: 38694 Sorted by residual: angle pdb=" C MET C 124 " pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 119.85 129.06 -9.21 1.01e+00 9.80e-01 8.32e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.16 -16.42 1.95e+00 2.62e-01 7.06e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.33 -13.49 1.91e+00 2.73e-01 4.96e+01 angle pdb=" C51 CDL N 201 " pdb=" CB5 CDL N 201 " pdb=" OB6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.30 -8.97 1.32e+00 5.72e-01 4.61e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.91 7.55 1.17e+00 7.36e-01 4.19e+01 ... (remaining 38689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 16942 35.83 - 71.67: 309 71.67 - 107.50: 32 107.50 - 143.33: 1 143.33 - 179.17: 4 Dihedral angle restraints: 17288 sinusoidal: 7226 harmonic: 10062 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 76.76 -179.17 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -137.84 51.84 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA PRO C 125 " pdb=" C PRO C 125 " pdb=" N GLU C 126 " pdb=" CA GLU C 126 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 17285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3798 0.078 - 0.156: 391 0.156 - 0.234: 14 0.234 - 0.312: 4 0.312 - 0.390: 1 Chirality restraints: 4208 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 -2.36 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C6 PLX C 303 " pdb=" C7 PLX C 303 " pdb=" O6 PLX C 303 " pdb=" O7 PLX C 303 " both_signs ideal model delta sigma weight residual False 2.01 2.32 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 4205 not shown) Planarity restraints: 4982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.022 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" C3N NDP J 401 " 0.388 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.085 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.211 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.112 2.00e-02 2.50e+03 2.01e-01 4.03e+02 pdb=" C2N NDP J 401 " 0.117 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.119 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.069 2.00e-02 2.50e+03 9.94e-02 9.88e+01 pdb=" C5N NDP J 401 " 0.123 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.123 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.069 2.00e-02 2.50e+03 ... (remaining 4979 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2325 2.74 - 3.28: 27580 3.28 - 3.82: 47110 3.82 - 4.36: 59426 4.36 - 4.90: 100105 Nonbonded interactions: 236546 Sorted by model distance: nonbonded pdb=" O VAL K 91 " pdb=" OG SER K 94 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR Q 226 " pdb=" O GLN Q 234 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG F 68 " pdb=" OD1 ASN M 359 " model vdw 2.202 3.120 nonbonded pdb=" NH2 ARG P 125 " pdb=" OD1 ASP P 201 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR M 385 " pdb=" OD1 ASP M 527 " model vdw 2.205 3.040 ... (remaining 236541 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.011 1.251 28608 Z= 0.339 Angle : 0.949 54.649 38777 Z= 0.401 Chirality : 0.047 0.390 4208 Planarity : 0.007 0.208 4982 Dihedral : 14.595 179.167 10813 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3439 helix: 0.69 (0.14), residues: 1326 sheet: 0.66 (0.27), residues: 377 loop : -0.48 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.048 0.002 TYR C 142 PHE 0.021 0.002 PHE C 67 TRP 0.070 0.002 TRP J 108 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (28570) covalent geometry : angle 0.75315 / 0.40 (38694) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 2.19538 / 1.25 ( 2) hydrogen bonds : bond 0.14733 / 9.82 ( 1107) hydrogen bonds : angle 6.39545 / 4.53 ( 3090) metal coordination : bond 0.23055 / 18.12 ( 36) metal coordination : angle 12.66146 / 7.37 ( 81) Misc. bond : bond 0.02083 / 1.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7008 (tppp) cc_final: 0.6607 (ttmt) REVERT: A 102 MET cc_start: 0.8561 (tpt) cc_final: 0.8296 (tmm) REVERT: E 57 LYS cc_start: 0.8512 (tttm) cc_final: 0.8007 (tttp) REVERT: E 69 LYS cc_start: 0.8244 (ttpt) cc_final: 0.8031 (mtmm) REVERT: F 41 TYR cc_start: 0.8482 (t80) cc_final: 0.8205 (t80) REVERT: I 10 LEU cc_start: 0.8155 (mt) cc_final: 0.7916 (mt) REVERT: J 220 MET cc_start: 0.7166 (mmp) cc_final: 0.6887 (mmm) REVERT: M 441 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: P 156 SER cc_start: 0.8800 (p) cc_final: 0.8531 (p) REVERT: Q 96 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8029 (ttt-90) outliers start: 0 outliers final: 2 residues processed: 507 average time/residue: 0.7176 time to fit residues: 415.5137 Evaluate side-chains 396 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain M residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN C 123 GLN J 154 GLN J 238 GLN K 110 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN ** M 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 31 ASN O 133 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN P 247 GLN T 63 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100047 restraints weight = 36701.245| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.44 r_work: 0.2911 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 28608 Z= 0.151 Angle : 0.834 63.650 38777 Z= 0.302 Chirality : 0.044 0.190 4208 Planarity : 0.005 0.069 4982 Dihedral : 9.283 179.817 3996 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 1.85 % Allowed : 9.00 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3439 helix: 1.11 (0.14), residues: 1322 sheet: 0.61 (0.27), residues: 385 loop : -0.42 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 195 TYR 0.028 0.001 TYR C 142 PHE 0.018 0.001 PHE Q 458 TRP 0.017 0.001 TRP J 108 HIS 0.015 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (28570) covalent geometry : angle 0.57650 / 0.30 (38694) SS BOND : bond 0.00599 / 0.32 ( 1) SS BOND : angle 2.58359 / 1.46 ( 2) hydrogen bonds : bond 0.04579 / 3.10 ( 1107) hydrogen bonds : angle 5.04215 / 3.59 ( 3090) metal coordination : bond 0.03844 / 3.11 ( 36) metal coordination : angle 13.19958 / 7.23 ( 81) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 409 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7150 (tppp) cc_final: 0.6690 (ttmm) REVERT: A 102 MET cc_start: 0.8719 (tpt) cc_final: 0.8233 (tpt) REVERT: B 50 MET cc_start: 0.8369 (tpp) cc_final: 0.7678 (tpt) REVERT: B 51 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8162 (tttm) REVERT: E 57 LYS cc_start: 0.8664 (tttm) cc_final: 0.8369 (tttp) REVERT: E 65 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: E 69 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8186 (mttt) REVERT: F 41 TYR cc_start: 0.8544 (t80) cc_final: 0.8202 (t80) REVERT: F 68 ARG cc_start: 0.8453 (ttt-90) cc_final: 0.8236 (ttt-90) REVERT: G 134 ASP cc_start: 0.7604 (p0) cc_final: 0.7275 (p0) REVERT: H 37 GLN cc_start: 0.8687 (mt0) cc_final: 0.8460 (mt0) REVERT: I 10 LEU cc_start: 0.8041 (mt) cc_final: 0.7768 (mt) REVERT: I 108 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8090 (ptpt) REVERT: J 205 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: J 220 MET cc_start: 0.7468 (mmp) cc_final: 0.7085 (mmm) REVERT: K 105 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7947 (ptp90) REVERT: M 42 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: M 466 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7479 (tp) REVERT: N 72 ASP cc_start: 0.8251 (t70) cc_final: 0.7842 (t0) REVERT: P 50 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (mtt90) REVERT: P 169 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: Q 96 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8413 (ttp-170) REVERT: Q 260 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8227 (mm-30) REVERT: Q 312 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8304 (p0) REVERT: W 7 LYS cc_start: 0.8781 (tptm) cc_final: 0.8248 (tppt) outliers start: 55 outliers final: 18 residues processed: 438 average time/residue: 0.6812 time to fit residues: 343.5301 Evaluate side-chains 406 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 466 LEU Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain T residue 77 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 319 optimal weight: 0.0050 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 278 optimal weight: 0.1980 chunk 207 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 48 ASN H 50 GLN J 154 GLN K 110 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS P 123 GLN P 247 GLN T 63 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098181 restraints weight = 36753.482| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.43 r_work: 0.2870 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 28608 Z= 0.186 Angle : 0.818 66.312 38777 Z= 0.304 Chirality : 0.045 0.193 4208 Planarity : 0.005 0.067 4982 Dihedral : 8.847 178.357 3992 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 2.25 % Allowed : 11.49 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3439 helix: 1.07 (0.14), residues: 1333 sheet: 0.57 (0.27), residues: 379 loop : -0.47 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 195 TYR 0.027 0.002 TYR C 142 PHE 0.017 0.002 PHE L 164 TRP 0.015 0.001 TRP M 422 HIS 0.013 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (28570) covalent geometry : angle 0.58523 / 0.30 (38694) SS BOND : bond 0.00631 / 0.33 ( 1) SS BOND : angle 2.52725 / 1.44 ( 2) hydrogen bonds : bond 0.04618 / 3.14 ( 1107) hydrogen bonds : angle 4.92361 / 3.51 ( 3090) metal coordination : bond 0.04410 / 3.60 ( 36) metal coordination : angle 12.52628 / 6.66 ( 81) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 404 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7312 (tppp) cc_final: 0.6759 (ttmm) REVERT: A 102 MET cc_start: 0.8808 (tpt) cc_final: 0.8224 (tpt) REVERT: C 119 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (ttpm) REVERT: E 57 LYS cc_start: 0.8604 (tttm) cc_final: 0.8392 (tttp) REVERT: E 69 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8190 (mttt) REVERT: E 114 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7074 (mpt90) REVERT: F 41 TYR cc_start: 0.8613 (t80) cc_final: 0.8344 (t80) REVERT: G 122 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8320 (mmm) REVERT: G 143 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: H 37 GLN cc_start: 0.8777 (mt0) cc_final: 0.8530 (mt0) REVERT: I 10 LEU cc_start: 0.8207 (mt) cc_final: 0.7920 (mt) REVERT: I 62 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: I 70 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (tmt) REVERT: I 108 LYS cc_start: 0.8312 (ptpp) cc_final: 0.8017 (ptpp) REVERT: J 220 MET cc_start: 0.7458 (mmp) cc_final: 0.7043 (mmm) REVERT: K 98 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7785 (mtm) REVERT: M 42 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: M 54 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: M 677 GLN cc_start: 0.6581 (mt0) cc_final: 0.6239 (tt0) REVERT: N 72 ASP cc_start: 0.8379 (t70) cc_final: 0.7980 (t0) REVERT: O 72 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: P 169 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: Q 260 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8174 (mm-30) REVERT: Q 312 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (p0) REVERT: W 7 LYS cc_start: 0.8802 (tptm) cc_final: 0.8273 (tppt) outliers start: 67 outliers final: 28 residues processed: 440 average time/residue: 0.6964 time to fit residues: 352.9183 Evaluate side-chains 416 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 329 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 275 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 0.0040 chunk 148 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN H 50 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 460 HIS ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN O 182 ASN P 123 GLN P 247 GLN T 63 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099117 restraints weight = 36696.163| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.41 r_work: 0.2932 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 28608 Z= 0.146 Angle : 0.774 62.326 38777 Z= 0.287 Chirality : 0.043 0.190 4208 Planarity : 0.005 0.072 4982 Dihedral : 8.564 178.988 3992 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.59 % Allowed : 13.23 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3439 helix: 1.12 (0.14), residues: 1336 sheet: 0.40 (0.26), residues: 395 loop : -0.43 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 195 TYR 0.016 0.001 TYR C 84 PHE 0.017 0.001 PHE L 164 TRP 0.015 0.001 TRP M 422 HIS 0.010 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (28570) covalent geometry : angle 0.55288 / 0.28 (38694) SS BOND : bond 0.00573 / 0.30 ( 1) SS BOND : angle 2.42892 / 1.38 ( 2) hydrogen bonds : bond 0.04187 / 2.85 ( 1107) hydrogen bonds : angle 4.82421 / 3.44 ( 3090) metal coordination : bond 0.03703 / 3.03 ( 36) metal coordination : angle 11.87321 / 6.32 ( 81) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 397 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7294 (tppp) cc_final: 0.6699 (ttmm) REVERT: A 134 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: B 50 MET cc_start: 0.8334 (tpp) cc_final: 0.7661 (tpt) REVERT: C 67 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: C 119 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8340 (ttpm) REVERT: E 69 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8241 (mttt) REVERT: F 41 TYR cc_start: 0.8568 (t80) cc_final: 0.8286 (t80) REVERT: H 26 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8576 (pp) REVERT: H 37 GLN cc_start: 0.8811 (mt0) cc_final: 0.8549 (mt0) REVERT: I 10 LEU cc_start: 0.8177 (mt) cc_final: 0.7891 (mt) REVERT: I 108 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7993 (ptpp) REVERT: J 205 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: J 220 MET cc_start: 0.7429 (mmp) cc_final: 0.6984 (mmm) REVERT: M 42 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.7925 (mmm) REVERT: M 54 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: M 677 GLN cc_start: 0.6560 (mt0) cc_final: 0.6235 (tt0) REVERT: N 43 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7815 (tttp) REVERT: N 72 ASP cc_start: 0.8427 (t70) cc_final: 0.8031 (t0) REVERT: P 169 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: Q 308 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.6041 (p90) REVERT: Q 312 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8321 (p0) REVERT: W 7 LYS cc_start: 0.8806 (tptm) cc_final: 0.8303 (tppt) outliers start: 77 outliers final: 28 residues processed: 441 average time/residue: 0.7351 time to fit residues: 373.4373 Evaluate side-chains 413 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain T residue 57 ASP Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 243 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS C 123 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 75 GLN P 123 GLN P 247 GLN T 63 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098699 restraints weight = 36765.099| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.37 r_work: 0.2910 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.251 28608 Z= 0.181 Angle : 0.768 56.630 38777 Z= 0.298 Chirality : 0.044 0.194 4208 Planarity : 0.005 0.069 4982 Dihedral : 8.404 178.281 3992 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 2.79 % Allowed : 14.01 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3439 helix: 1.08 (0.14), residues: 1345 sheet: 0.39 (0.26), residues: 401 loop : -0.48 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.018 0.002 TYR C 84 PHE 0.017 0.002 PHE L 164 TRP 0.015 0.001 TRP M 422 HIS 0.010 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (28570) covalent geometry : angle 0.57631 / 0.29 (38694) SS BOND : bond 0.00635 / 0.33 ( 1) SS BOND : angle 2.42683 / 1.38 ( 2) hydrogen bonds : bond 0.04462 / 3.04 ( 1107) hydrogen bonds : angle 4.86402 / 3.47 ( 3090) metal coordination : bond 0.04424 / 3.62 ( 36) metal coordination : angle 11.12312 / 5.94 ( 81) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7363 (tppp) cc_final: 0.6726 (ttmm) REVERT: A 102 MET cc_start: 0.8823 (tpt) cc_final: 0.8511 (tpt) REVERT: A 134 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: A 296 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 67 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: C 119 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8289 (ttpm) REVERT: E 69 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8165 (mttt) REVERT: E 101 THR cc_start: 0.8887 (t) cc_final: 0.8557 (t) REVERT: F 41 TYR cc_start: 0.8557 (t80) cc_final: 0.8255 (t80) REVERT: G 143 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: H 26 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8529 (pp) REVERT: H 37 GLN cc_start: 0.8788 (mt0) cc_final: 0.8512 (mt0) REVERT: I 10 LEU cc_start: 0.8101 (mt) cc_final: 0.7810 (mt) REVERT: I 62 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: I 108 LYS cc_start: 0.8304 (ptpp) cc_final: 0.8023 (ptpp) REVERT: M 42 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7892 (mmm) REVERT: M 54 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: M 215 MET cc_start: 0.7221 (mmt) cc_final: 0.6866 (mmp) REVERT: M 655 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7874 (mtt180) REVERT: M 677 GLN cc_start: 0.6798 (mt0) cc_final: 0.6270 (tt0) REVERT: N 72 ASP cc_start: 0.8371 (t70) cc_final: 0.7985 (t0) REVERT: P 169 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: Q 185 MET cc_start: 0.8844 (tpt) cc_final: 0.8621 (tpt) REVERT: Q 308 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.5904 (p90) REVERT: Q 312 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (p0) REVERT: W 7 LYS cc_start: 0.8756 (tptm) cc_final: 0.8231 (tppt) outliers start: 83 outliers final: 35 residues processed: 440 average time/residue: 0.7617 time to fit residues: 384.5040 Evaluate side-chains 419 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN N 13 GLN O 133 GLN P 123 GLN P 247 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101586 restraints weight = 36497.614| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.36 r_work: 0.2956 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 28608 Z= 0.125 Angle : 0.744 57.266 38777 Z= 0.275 Chirality : 0.042 0.185 4208 Planarity : 0.004 0.064 4982 Dihedral : 7.978 179.951 3992 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.79 % Allowed : 14.65 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3439 helix: 1.19 (0.14), residues: 1352 sheet: 0.28 (0.26), residues: 385 loop : -0.40 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 109 TYR 0.014 0.001 TYR C 84 PHE 0.015 0.001 PHE Q 458 TRP 0.015 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (28570) covalent geometry : angle 0.53096 / 0.27 (38694) SS BOND : bond 0.00523 / 0.28 ( 1) SS BOND : angle 2.36250 / 1.35 ( 2) hydrogen bonds : bond 0.03843 / 2.61 ( 1107) hydrogen bonds : angle 4.71336 / 3.36 ( 3090) metal coordination : bond 0.03083 / 2.52 ( 36) metal coordination : angle 11.41022 / 6.13 ( 81) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 400 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7355 (tppp) cc_final: 0.6706 (ttmm) REVERT: A 149 MET cc_start: 0.8677 (mtm) cc_final: 0.8341 (mtp) REVERT: A 296 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8876 (tt) REVERT: B 50 MET cc_start: 0.8359 (tpp) cc_final: 0.7727 (tpt) REVERT: C 67 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: C 119 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (ttpm) REVERT: E 65 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: E 69 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8157 (mttt) REVERT: E 101 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8477 (t) REVERT: F 41 TYR cc_start: 0.8526 (t80) cc_final: 0.8304 (t80) REVERT: G 143 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: H 26 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (pp) REVERT: H 37 GLN cc_start: 0.8809 (mt0) cc_final: 0.8561 (mt0) REVERT: I 10 LEU cc_start: 0.8109 (mt) cc_final: 0.7808 (mt) REVERT: I 108 LYS cc_start: 0.8250 (ptpp) cc_final: 0.8009 (ptpp) REVERT: J 79 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.7948 (tp-100) REVERT: J 102 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8792 (mm-40) REVERT: J 220 MET cc_start: 0.7425 (mmp) cc_final: 0.6954 (mmm) REVERT: J 271 TYR cc_start: 0.8460 (m-80) cc_final: 0.8241 (m-80) REVERT: M 42 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.7875 (mmm) REVERT: M 655 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7890 (mtt180) REVERT: M 677 GLN cc_start: 0.6719 (mt0) cc_final: 0.6256 (tt0) REVERT: O 72 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: P 85 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7689 (mt-10) REVERT: Q 80 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7524 (pt) REVERT: Q 185 MET cc_start: 0.8870 (tpt) cc_final: 0.8643 (tpt) REVERT: Q 308 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.5985 (p90) REVERT: Q 312 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (p0) REVERT: Q 455 ASP cc_start: 0.7418 (t70) cc_final: 0.7217 (t70) REVERT: W 7 LYS cc_start: 0.8790 (tptm) cc_final: 0.8252 (tppt) outliers start: 83 outliers final: 35 residues processed: 447 average time/residue: 0.6505 time to fit residues: 336.2529 Evaluate side-chains 429 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 320 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 246 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 255 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN H 76 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 123 GLN P 247 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101846 restraints weight = 36363.801| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.35 r_work: 0.2937 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 28608 Z= 0.121 Angle : 0.737 55.760 38777 Z= 0.274 Chirality : 0.042 0.182 4208 Planarity : 0.004 0.060 4982 Dihedral : 7.729 179.945 3992 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.35 % Allowed : 15.79 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3439 helix: 1.25 (0.14), residues: 1348 sheet: 0.26 (0.26), residues: 385 loop : -0.35 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.016 0.001 TYR C 84 PHE 0.015 0.001 PHE L 164 TRP 0.014 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (28570) covalent geometry : angle 0.53313 / 0.27 (38694) SS BOND : bond 0.00497 / 0.26 ( 1) SS BOND : angle 2.26132 / 1.29 ( 2) hydrogen bonds : bond 0.03744 / 2.54 ( 1107) hydrogen bonds : angle 4.67218 / 3.33 ( 3090) metal coordination : bond 0.03064 / 2.51 ( 36) metal coordination : angle 11.14660 / 5.99 ( 81) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 390 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7374 (tppp) cc_final: 0.6731 (ttmm) REVERT: A 102 MET cc_start: 0.8735 (tpt) cc_final: 0.8344 (tpt) REVERT: A 121 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: A 149 MET cc_start: 0.8611 (mtm) cc_final: 0.8385 (mtp) REVERT: A 296 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8838 (tt) REVERT: B 50 MET cc_start: 0.8263 (tpp) cc_final: 0.7653 (tpt) REVERT: E 65 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: E 69 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8069 (mttt) REVERT: E 99 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (mp10) REVERT: E 101 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8431 (t) REVERT: F 41 TYR cc_start: 0.8478 (t80) cc_final: 0.8237 (t80) REVERT: G 133 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7187 (tp) REVERT: G 143 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: H 26 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8504 (pp) REVERT: H 37 GLN cc_start: 0.8781 (mt0) cc_final: 0.8513 (mt0) REVERT: I 10 LEU cc_start: 0.7909 (mt) cc_final: 0.7586 (mt) REVERT: I 70 MET cc_start: 0.8467 (tmt) cc_final: 0.8148 (tmt) REVERT: J 102 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8862 (mm-40) REVERT: J 220 MET cc_start: 0.7346 (mmp) cc_final: 0.6875 (mmm) REVERT: J 271 TYR cc_start: 0.8392 (m-80) cc_final: 0.8155 (m-80) REVERT: M 42 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: M 54 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: M 77 MET cc_start: 0.8994 (tpt) cc_final: 0.8489 (tpt) REVERT: M 655 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7911 (mtt180) REVERT: M 677 GLN cc_start: 0.6695 (mt0) cc_final: 0.6214 (tt0) REVERT: O 72 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: Q 185 MET cc_start: 0.8819 (tpt) cc_final: 0.8602 (tpt) REVERT: Q 308 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.6086 (p90) outliers start: 70 outliers final: 32 residues processed: 432 average time/residue: 0.6954 time to fit residues: 345.8240 Evaluate side-chains 423 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 379 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain T residue 57 ASP Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 13 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 308 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN J 154 GLN K 110 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 123 GLN P 247 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101333 restraints weight = 36739.916| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.32 r_work: 0.2920 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 28608 Z= 0.122 Angle : 0.731 54.703 38777 Z= 0.273 Chirality : 0.042 0.183 4208 Planarity : 0.004 0.057 4982 Dihedral : 7.485 179.933 3992 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.35 % Allowed : 15.89 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3439 helix: 1.28 (0.14), residues: 1348 sheet: 0.28 (0.26), residues: 385 loop : -0.34 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 109 TYR 0.013 0.001 TYR C 84 PHE 0.016 0.001 PHE L 164 TRP 0.014 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (28570) covalent geometry : angle 0.53179 / 0.27 (38694) SS BOND : bond 0.00507 / 0.27 ( 1) SS BOND : angle 2.23015 / 1.27 ( 2) hydrogen bonds : bond 0.03699 / 2.51 ( 1107) hydrogen bonds : angle 4.64943 / 3.31 ( 3090) metal coordination : bond 0.03055 / 2.50 ( 36) metal coordination : angle 10.97983 / 5.90 ( 81) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 390 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7379 (tppp) cc_final: 0.6725 (ttmm) REVERT: A 102 MET cc_start: 0.8816 (tpt) cc_final: 0.8449 (tpt) REVERT: A 296 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 50 MET cc_start: 0.8246 (tpp) cc_final: 0.7655 (tpt) REVERT: E 65 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: E 69 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8100 (mttt) REVERT: E 99 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: E 101 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8459 (t) REVERT: G 133 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7263 (tp) REVERT: G 143 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: H 26 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8546 (pp) REVERT: H 37 GLN cc_start: 0.8802 (mt0) cc_final: 0.8541 (mt0) REVERT: I 10 LEU cc_start: 0.7934 (mt) cc_final: 0.7629 (mt) REVERT: I 70 MET cc_start: 0.8393 (tmt) cc_final: 0.8146 (tmt) REVERT: I 108 LYS cc_start: 0.8325 (ptpp) cc_final: 0.8093 (ptpt) REVERT: J 102 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8860 (mm-40) REVERT: J 220 MET cc_start: 0.7390 (mmp) cc_final: 0.6903 (mmm) REVERT: J 271 TYR cc_start: 0.8410 (m-80) cc_final: 0.8164 (m-80) REVERT: M 42 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.7930 (mmm) REVERT: M 54 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: M 655 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7931 (mtt180) REVERT: M 677 GLN cc_start: 0.6702 (mt0) cc_final: 0.6236 (tt0) REVERT: O 72 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: Q 185 MET cc_start: 0.8865 (tpt) cc_final: 0.8565 (tpt) REVERT: Q 308 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.6906 (p90) REVERT: Q 455 ASP cc_start: 0.7657 (t70) cc_final: 0.7437 (t70) REVERT: W 7 LYS cc_start: 0.8767 (tptm) cc_final: 0.8192 (tppt) outliers start: 70 outliers final: 37 residues processed: 431 average time/residue: 0.6788 time to fit residues: 337.2204 Evaluate side-chains 430 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 501 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 266 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN H 50 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 123 GLN T 101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.097716 restraints weight = 36790.732| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.39 r_work: 0.2902 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.289 28608 Z= 0.221 Angle : 0.778 50.949 38777 Z= 0.316 Chirality : 0.046 0.199 4208 Planarity : 0.005 0.052 4982 Dihedral : 7.669 177.718 3992 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.35 % Allowed : 16.53 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3439 helix: 1.09 (0.14), residues: 1338 sheet: 0.32 (0.27), residues: 389 loop : -0.52 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 109 TYR 0.017 0.002 TYR C 84 PHE 0.018 0.002 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (28570) covalent geometry : angle 0.61700 / 0.31 (38694) SS BOND : bond 0.00710 / 0.37 ( 1) SS BOND : angle 2.22459 / 1.27 ( 2) hydrogen bonds : bond 0.04651 / 3.18 ( 1107) hydrogen bonds : angle 4.88463 / 3.48 ( 3090) metal coordination : bond 0.05097 / 4.17 ( 36) metal coordination : angle 10.37789 / 5.55 ( 81) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 384 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7385 (tppp) cc_final: 0.6726 (ttpt) REVERT: A 185 ASN cc_start: 0.6930 (m-40) cc_final: 0.6664 (m110) REVERT: A 296 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 50 MET cc_start: 0.8268 (tpp) cc_final: 0.7638 (tpt) REVERT: C 67 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: E 69 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8185 (mttt) REVERT: E 101 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8599 (t) REVERT: G 133 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7302 (tp) REVERT: G 143 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: H 26 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8558 (pp) REVERT: H 37 GLN cc_start: 0.8798 (mt0) cc_final: 0.8519 (mt0) REVERT: I 10 LEU cc_start: 0.8212 (mt) cc_final: 0.7958 (mt) REVERT: I 70 MET cc_start: 0.8578 (tmt) cc_final: 0.8245 (tmt) REVERT: I 108 LYS cc_start: 0.8332 (ptpp) cc_final: 0.8116 (ptpt) REVERT: J 79 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8050 (tp-100) REVERT: J 220 MET cc_start: 0.7457 (mmp) cc_final: 0.7036 (mmm) REVERT: J 351 GLU cc_start: 0.8188 (pt0) cc_final: 0.7979 (pt0) REVERT: M 42 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: M 54 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: M 77 MET cc_start: 0.9069 (tpt) cc_final: 0.8524 (tpt) REVERT: M 441 ARG cc_start: 0.8618 (ttp-170) cc_final: 0.8218 (ttt180) REVERT: M 655 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7956 (mtt180) REVERT: M 677 GLN cc_start: 0.6947 (mt0) cc_final: 0.6544 (tt0) REVERT: O 72 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: P 169 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: Q 308 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.6019 (p90) REVERT: Q 312 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (p0) REVERT: W 7 LYS cc_start: 0.8800 (tptm) cc_final: 0.8284 (tppt) outliers start: 70 outliers final: 38 residues processed: 426 average time/residue: 0.6802 time to fit residues: 334.4538 Evaluate side-chains 421 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 370 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 501 ARG Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 67 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099864 restraints weight = 36478.404| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.29 r_work: 0.2930 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 28608 Z= 0.177 Angle : 0.772 54.214 38777 Z= 0.304 Chirality : 0.044 0.193 4208 Planarity : 0.005 0.050 4982 Dihedral : 7.567 178.837 3992 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 17.16 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3439 helix: 1.09 (0.14), residues: 1345 sheet: 0.27 (0.26), residues: 395 loop : -0.53 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 109 TYR 0.018 0.002 TYR E 40 PHE 0.015 0.002 PHE B 175 TRP 0.014 0.001 TRP M 422 HIS 0.009 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (28570) covalent geometry : angle 0.59210 / 0.30 (38694) SS BOND : bond 0.00613 / 0.32 ( 1) SS BOND : angle 2.24576 / 1.28 ( 2) hydrogen bonds : bond 0.04346 / 2.97 ( 1107) hydrogen bonds : angle 4.84911 / 3.45 ( 3090) metal coordination : bond 0.04154 / 3.40 ( 36) metal coordination : angle 10.86028 / 5.79 ( 81) Misc. bond : bond 0.00006 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 375 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7375 (tppp) cc_final: 0.6728 (ttpt) REVERT: A 185 ASN cc_start: 0.6973 (m-40) cc_final: 0.6638 (m110) REVERT: A 296 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 50 MET cc_start: 0.8301 (tpp) cc_final: 0.7660 (tpt) REVERT: C 67 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: C 99 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: E 69 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8209 (mttt) REVERT: E 101 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8550 (t) REVERT: G 133 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7330 (tp) REVERT: G 143 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: H 26 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8584 (pp) REVERT: H 37 GLN cc_start: 0.8775 (mt0) cc_final: 0.8498 (mt0) REVERT: I 10 LEU cc_start: 0.8240 (mt) cc_final: 0.7938 (mt) REVERT: I 70 MET cc_start: 0.8458 (tmt) cc_final: 0.8166 (tmt) REVERT: I 108 LYS cc_start: 0.8289 (ptpp) cc_final: 0.8064 (ptpt) REVERT: J 220 MET cc_start: 0.7484 (mmp) cc_final: 0.7168 (mmm) REVERT: M 42 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: M 54 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: M 77 MET cc_start: 0.8965 (tpt) cc_final: 0.8568 (tpt) REVERT: M 441 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8219 (ttt180) REVERT: M 655 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7920 (mtt180) REVERT: M 677 GLN cc_start: 0.6917 (mt0) cc_final: 0.6552 (tt0) REVERT: O 72 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: Q 308 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.5966 (p90) REVERT: Q 312 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8235 (p0) REVERT: W 7 LYS cc_start: 0.8770 (tptm) cc_final: 0.8279 (tppt) outliers start: 61 outliers final: 37 residues processed: 414 average time/residue: 0.6876 time to fit residues: 330.6243 Evaluate side-chains 423 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 374 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 501 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 170 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN H 50 GLN J 79 GLN J 154 GLN K 110 HIS L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 133 GLN P 75 GLN P 123 GLN T 101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099850 restraints weight = 36624.519| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.33 r_work: 0.2955 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 28608 Z= 0.131 Angle : 0.750 55.479 38777 Z= 0.284 Chirality : 0.043 0.184 4208 Planarity : 0.004 0.050 4982 Dihedral : 7.321 179.820 3992 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 1.85 % Allowed : 17.53 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3439 helix: 1.21 (0.14), residues: 1347 sheet: 0.17 (0.27), residues: 380 loop : -0.42 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 109 TYR 0.020 0.001 TYR F 41 PHE 0.016 0.001 PHE L 164 TRP 0.015 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (28570) covalent geometry : angle 0.55304 / 0.28 (38694) SS BOND : bond 0.00515 / 0.27 ( 1) SS BOND : angle 2.28577 / 1.30 ( 2) hydrogen bonds : bond 0.03847 / 2.62 ( 1107) hydrogen bonds : angle 4.74030 / 3.36 ( 3090) metal coordination : bond 0.03186 / 2.60 ( 36) metal coordination : angle 11.09220 / 5.95 ( 81) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8936.27 seconds wall clock time: 152 minutes 54.39 seconds (9174.39 seconds total)