Starting phenix.real_space_refine on Mon May 26 18:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_32205.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_32205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_32205.map" model { file = "/net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_32205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyh_32205/05_2025/7vyh_32205.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} 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: 15.01, per 1000 atoms: 0.54 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: 7.20 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="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: 3.28 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: 9.48 Time building geometry restraints manager: 8.38 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: 38399 3.32 - 6.64: 238 6.64 - 9.96: 38 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 - 33.21: 16869 33.21 - 66.41: 394 66.41 - 99.62: 49 99.62 - 132.82: 5 132.82 - 166.03: 3 Dihedral angle restraints: 17320 sinusoidal: 7258 harmonic: 10062 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -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 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 17317 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: 4983 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 4980 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 72.280 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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= 0.343 Angle : 0.955 54.649 38777 Z= 0.402 Chirality : 0.047 0.390 4208 Planarity : 0.007 0.208 4983 Dihedral : 14.767 166.031 10845 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.070 0.002 TRP J 108 HIS 0.008 0.001 HIS J 37 PHE 0.021 0.002 PHE C 67 TYR 0.048 0.002 TYR C 142 ARG 0.007 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.14733 ( 1107) hydrogen bonds : angle 6.39545 ( 3090) metal coordination : bond 0.23055 ( 36) metal coordination : angle 12.66146 ( 81) SS BOND : bond 0.00414 ( 1) SS BOND : angle 2.19538 ( 2) covalent geometry : bond 0.00689 (28570) covalent geometry : angle 0.76055 (38694) Misc. bond : bond 0.02083 ( 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 : 2.885 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: 0.7917 (mt) REVERT: J 220 MET cc_start: 0.7166 (mmp) cc_final: 0.6888 (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: 0.8030 (ttt-90) outliers start: 0 outliers final: 2 residues processed: 507 average time/residue: 1.6537 time to fit residues: 956.4194 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 : 4.706 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3705 > 50: distance: 73 - 151: 36.773 distance: 76 - 148: 37.565 distance: 95 - 101: 33.913 distance: 101 - 102: 48.637 distance: 101 - 107: 58.509 distance: 102 - 103: 58.252 distance: 102 - 105: 48.386 distance: 103 - 104: 39.955 distance: 103 - 108: 65.518 distance: 106 - 107: 47.471 distance: 108 - 109: 33.113 distance: 109 - 110: 43.238 distance: 109 - 112: 62.476 distance: 110 - 111: 28.678 distance: 110 - 116: 41.614 distance: 112 - 113: 58.084 distance: 113 - 114: 39.378 distance: 113 - 115: 35.444 distance: 117 - 120: 67.820 distance: 118 - 119: 55.494 distance: 118 - 124: 57.710 distance: 120 - 121: 41.580 distance: 121 - 122: 32.983 distance: 122 - 123: 26.153 distance: 124 - 125: 41.388 distance: 125 - 126: 39.967 distance: 126 - 127: 40.654 distance: 128 - 129: 39.695 distance: 129 - 130: 60.293 distance: 129 - 132: 42.697 distance: 130 - 131: 43.997 distance: 130 - 142: 20.795 distance: 132 - 133: 40.722 distance: 133 - 135: 51.389 distance: 134 - 136: 60.228 distance: 135 - 137: 47.756 distance: 135 - 138: 47.954 distance: 136 - 137: 57.917 distance: 137 - 139: 59.138 distance: 138 - 140: 54.237 distance: 139 - 141: 58.475 distance: 140 - 141: 32.505 distance: 142 - 143: 50.205 distance: 143 - 144: 31.066 distance: 143 - 146: 31.830 distance: 144 - 145: 57.252 distance: 144 - 148: 55.907 distance: 146 - 147: 62.217 distance: 148 - 149: 26.083 distance: 149 - 150: 53.955 distance: 149 - 152: 32.371 distance: 150 - 151: 50.612 distance: 150 - 154: 6.259 distance: 152 - 153: 60.824 distance: 155 - 156: 46.921 distance: 155 - 158: 70.018 distance: 156 - 157: 42.930 distance: 156 - 161: 33.416 distance: 158 - 160: 39.084 distance: 161 - 162: 20.457 distance: 162 - 163: 27.756 distance: 162 - 165: 44.382 distance: 163 - 164: 48.174 distance: 163 - 166: 14.453 distance: 166 - 167: 61.869 distance: 167 - 168: 47.846 distance: 167 - 170: 29.100 distance: 168 - 169: 40.191 distance: 168 - 174: 31.835 distance: 170 - 171: 21.293 distance: 171 - 172: 46.800 distance: 171 - 173: 33.620