Starting phenix.real_space_refine on Fri Mar 6 09:01:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbn_31883/03_2026/7vbn_31883.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17945 2.51 5 N 4933 2.21 5 O 5935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29042 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2651 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 22, 'TRANS': 308} Chain breaks: 1 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "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} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "Q" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "T" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.069 48.957 101.539 1.00 15.19 S ATOM 3048 SG CYS A 425 47.366 45.608 107.227 1.00 19.85 S ATOM 2726 SG CYS A 385 44.793 44.759 101.427 1.00 16.17 S ATOM 2687 SG CYS A 379 42.853 49.736 105.525 1.00 18.54 S ATOM 3949 SG CYS B 113 37.170 66.153 67.383 1.00 12.28 S ATOM 3968 SG CYS B 116 42.333 63.605 71.030 1.00 11.43 S ATOM 3991 SG CYS B 119 43.300 66.387 65.534 1.00 12.07 S ATOM 4320 SG CYS B 162 40.595 60.679 66.079 1.00 11.23 S ATOM 4018 SG CYS B 123 49.398 69.108 61.155 1.00 12.12 S ATOM 4244 SG CYS B 152 47.588 67.654 55.151 1.00 11.12 S ATOM 4291 SG CYS B 158 45.561 63.841 60.064 1.00 21.77 S ATOM 4270 SG CYS B 155 51.534 63.802 58.534 1.00 21.77 S ATOM 5712 SG CYS C 166 53.868 67.592 51.043 1.00 12.22 S ATOM 4984 SG CYS C 72 54.635 69.193 44.769 1.00 11.91 S ATOM 4978 SG CYS C 71 59.643 67.141 47.359 1.00 11.43 S ATOM 5482 SG CYS C 136 56.606 72.195 49.719 1.00 11.71 S ATOM 14830 SG CYS M 131 41.573 63.318 83.061 1.00 11.42 S ATOM 14809 SG CYS M 128 45.036 58.768 79.733 1.00 9.41 S ATOM 14870 SG CYS M 137 47.269 61.934 85.093 1.00 10.65 S ATOM 15202 SG CYS M 179 45.622 61.879 96.276 1.00 13.58 S ATOM 15556 SG CYS M 226 42.557 64.714 92.030 1.00 11.66 S ATOM 15226 SG CYS M 182 40.282 64.582 98.094 1.00 13.66 S ATOM 15179 SG CYS M 176 39.816 59.196 94.512 1.00 12.01 S ATOM 14427 SG CYS M 78 56.931 56.515 99.687 1.00 13.95 S ATOM 14528 SG CYS M 92 55.292 58.740 102.049 1.00 13.95 S ATOM 14316 SG CYS M 64 50.971 58.733 99.923 1.00 10.92 S ATOM 14402 SG CYS M 75 51.854 57.007 96.696 1.00 11.41 S ATOM 21365 SG CYS O 135 31.412 31.881 109.006 1.00 36.76 S ATOM 21399 SG CYS O 140 31.259 28.566 110.196 1.00 37.99 S ATOM 21679 SG CYS O 176 35.831 33.216 111.746 1.00 36.12 S ATOM 21702 SG CYS O 180 36.335 29.975 112.900 1.00 39.78 S ATOM 27460 SG CYS T 86 29.296 52.932 74.880 1.00 17.63 S ATOM 27638 SG CYS T 111 30.725 56.397 75.793 1.00 18.43 S Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 29042 At special positions: 0 Unit cell: (124.607, 139.109, 156.833, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 11 15.00 Mg 1 11.99 O 5935 8.00 N 4933 7.00 C 17945 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 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="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " 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="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 32 sheets defined 45.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.702A pdb=" N GLY A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.544A 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: 3.774A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.666A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.522A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.642A pdb=" N GLY A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) 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 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.837A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.689A 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: 3.537A 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: 5.936A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.788A pdb=" N ALA C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 80 removed outlier: 4.148A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.625A pdb=" N SER C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.837A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.511A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 48 removed outlier: 6.950A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.667A 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 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 4.019A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.598A 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: 3.609A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 92 removed outlier: 3.563A 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 121 removed outlier: 3.683A 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 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 231 through 233 No H-bonds generated for 'chain 'J' and resid 231 through 233' Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 294 through 308 removed outlier: 3.567A pdb=" N PHE J 305 " --> pdb=" O VAL J 301 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER J 308 " --> pdb=" O LEU J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 324 Processing helix chain 'J' and resid 335 through 339 Processing helix chain 'J' and resid 344 through 354 removed outlier: 4.034A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.874A pdb=" N HIS K 78 " --> pdb=" O ASN K 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.328A pdb=" N GLY L 66 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.570A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 57 removed outlier: 3.720A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.552A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.520A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.056A pdb=" N ASP M 224 " --> pdb=" O GLY M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 245 Processing helix chain 'M' and resid 287 through 293 Processing helix chain 'M' and resid 294 through 299 Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.578A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.709A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 426 removed outlier: 3.522A pdb=" N ASP M 426 " --> pdb=" O TRP M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 458 removed outlier: 4.033A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 4.079A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 528 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.096A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 3.557A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 655 " --> pdb=" O ASN M 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 655' Processing helix chain 'M' and resid 664 through 672 Processing helix chain 'M' and resid 690 through 694 Processing helix chain 'M' and resid 698 through 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 31 removed outlier: 4.254A pdb=" N GLY N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.583A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 69 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.652A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.803A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.097A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 51 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 3.959A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG P 168 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.846A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 140 Proline residue: Q 134 - end of helix removed outlier: 4.073A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.921A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 194 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 3.947A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.514A pdb=" N ASP Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.807A 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: 3.633A 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: 4.023A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.641A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 removed outlier: 3.585A pdb=" N VAL Q 461 " --> pdb=" O VAL Q 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.597A 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: 6.242A pdb=" N ALA A 154 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 198 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE A 156 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 removed outlier: 7.545A pdb=" N VAL A 354 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN A 277 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 356 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A 279 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASP A 358 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.199A pdb=" N LYS B 39 " --> pdb=" O ILE Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.493A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.261A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 58 removed outlier: 8.713A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 67 through 71 removed outlier: 5.301A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 113 " --> pdb=" O ASN P 131 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU P 111 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.572A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'J' and resid 227 through 229 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: 9.268A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 4.098A 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: 7.777A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.540A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.402A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'N' and resid 37 through 41 removed outlier: 5.787A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 169 through 174 removed outlier: 3.805A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.729A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC9, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.654A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD2, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD3, first strand: chain 'T' and resid 30 through 31 removed outlier: 3.989A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 77 through 78 Processing sheet with id=AD5, first strand: chain 'T' and resid 83 through 86 1139 hydrogen bonds defined for protein. 3177 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: 6.06 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 11710 1.41 - 1.63: 16937 1.63 - 1.85: 266 1.85 - 2.08: 2 2.08 - 2.30: 80 Bond restraints: 28995 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.634 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CB7 CDL N 201 " pdb=" OB8 CDL N 201 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 ... (remaining 28990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 38999 3.36 - 6.73: 238 6.73 - 10.09: 35 10.09 - 13.46: 9 13.46 - 16.82: 8 Bond angle restraints: 39289 Sorted by residual: angle pdb=" N PRO O 165 " pdb=" CD PRO O 165 " pdb=" CG PRO O 165 " ideal model delta sigma weight residual 103.20 89.30 13.90 1.50e+00 4.44e-01 8.59e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 120.66 -16.82 1.91e+00 2.73e-01 7.72e+01 angle pdb=" N PHE Q 458 " pdb=" CA PHE Q 458 " pdb=" C PHE Q 458 " ideal model delta sigma weight residual 111.28 119.34 -8.06 1.09e+00 8.42e-01 5.46e+01 angle pdb=" CA PRO O 165 " pdb=" CB PRO O 165 " pdb=" CG PRO O 165 " ideal model delta sigma weight residual 104.50 90.50 14.00 1.90e+00 2.77e-01 5.43e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 121.67 -13.93 1.95e+00 2.62e-01 5.08e+01 ... (remaining 39284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 16941 35.37 - 70.74: 593 70.74 - 106.11: 49 106.11 - 141.48: 3 141.48 - 176.84: 6 Dihedral angle restraints: 17592 sinusoidal: 7429 harmonic: 10163 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 -141.53 55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA SER O 224 " pdb=" C SER O 224 " pdb=" N CYS O 225 " pdb=" CA CYS O 225 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" C PHE Q 458 " pdb=" N PHE Q 458 " pdb=" CA PHE Q 458 " pdb=" CB PHE Q 458 " ideal model delta harmonic sigma weight residual -122.60 -135.18 12.58 0 2.50e+00 1.60e-01 2.53e+01 ... (remaining 17589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4150 0.111 - 0.222: 101 0.222 - 0.333: 6 0.333 - 0.443: 0 0.443 - 0.554: 2 Chirality restraints: 4259 Sorted by residual: chirality pdb=" CA PHE Q 458 " pdb=" N PHE Q 458 " pdb=" C PHE Q 458 " pdb=" CB PHE Q 458 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA TYR Q 141 " pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CB TYR Q 141 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.87e+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 2.33 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4256 not shown) Planarity restraints: 5054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 104 " 0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO A 105 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 154 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO L 155 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO L 155 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 155 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG Q 228 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.68e+00 pdb=" N PRO Q 229 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 229 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 229 " 0.040 5.00e-02 4.00e+02 ... (remaining 5051 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 419 2.58 - 3.16: 23746 3.16 - 3.74: 49539 3.74 - 4.32: 72750 4.32 - 4.90: 112102 Nonbonded interactions: 258556 Sorted by model distance: nonbonded pdb=" OE1 GLU Q 281 " pdb=" O HOH Q 501 " model vdw 2.002 3.040 nonbonded pdb=" O ALA Q 426 " pdb=" O HOH Q 502 " model vdw 2.066 3.040 nonbonded pdb=" N LYS C 188 " pdb=" OE2 GLU J 87 " model vdw 2.090 3.120 nonbonded pdb=" O HIS M 460 " pdb=" OG SER M 463 " model vdw 2.099 3.040 nonbonded pdb=" O ALA Q 402 " pdb=" O HOH Q 503 " model vdw 2.104 3.040 ... (remaining 258551 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: 8.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 34.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.503 29034 Z= 0.438 Angle : 0.858 37.316 39372 Z= 0.411 Chirality : 0.047 0.554 4259 Planarity : 0.005 0.097 5054 Dihedral : 17.146 176.844 11055 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 1.39 % Allowed : 13.82 % Favored : 84.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.80 % 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: 0.39 (0.14), residues: 3477 helix: 1.03 (0.14), residues: 1334 sheet: 0.25 (0.26), residues: 363 loop : -0.26 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 191 TYR 0.024 0.001 TYR C 142 PHE 0.017 0.001 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00646 (28995) covalent geometry : angle 0.76080 (39289) SS BOND : bond 0.00745 ( 1) SS BOND : angle 2.74192 ( 2) hydrogen bonds : bond 0.14254 ( 1139) hydrogen bonds : angle 6.33693 ( 3177) metal coordination : bond 0.04649 ( 36) metal coordination : angle 8.76967 ( 81) Misc. bond : bond 0.35588 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 419 time to evaluate : 1.206 Fit side-chains REVERT: A 37 ASP cc_start: 0.7383 (t0) cc_final: 0.7116 (t0) REVERT: E 116 THR cc_start: 0.8366 (m) cc_final: 0.8149 (t) REVERT: H 40 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7682 (mmtm) REVERT: I 70 MET cc_start: 0.8292 (tmt) cc_final: 0.7868 (tmt) REVERT: J 316 ARG cc_start: 0.8302 (mtm110) cc_final: 0.8013 (mtm110) REVERT: M 467 LYS cc_start: 0.7951 (tttm) cc_final: 0.7716 (tttm) REVERT: M 513 MET cc_start: 0.8179 (tpt) cc_final: 0.7777 (tpt) REVERT: O 165 PRO cc_start: 0.8252 (OUTLIER) cc_final: 0.8008 (Cg_exo) outliers start: 42 outliers final: 27 residues processed: 452 average time/residue: 0.8728 time to fit residues: 448.7257 Evaluate side-chains 430 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 401 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 165 PRO Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN J 71 ASN J 79 GLN K 77 GLN M 39 GLN M 464 GLN O 123 ASN O 153 GLN P 236 ASN Q 147 ASN Q 160 ASN Q 182 ASN T 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103355 restraints weight = 30462.864| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.22 r_work: 0.2983 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.364 29034 Z= 0.177 Angle : 0.730 30.709 39372 Z= 0.324 Chirality : 0.046 0.189 4259 Planarity : 0.005 0.075 5054 Dihedral : 11.450 173.794 4180 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.94 % Allowed : 13.29 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3477 helix: 1.15 (0.14), residues: 1345 sheet: 0.17 (0.26), residues: 356 loop : -0.25 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 138 TYR 0.021 0.002 TYR J 180 PHE 0.022 0.002 PHE L 164 TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00397 (28995) covalent geometry : angle 0.61577 (39289) SS BOND : bond 0.01113 ( 1) SS BOND : angle 3.28239 ( 2) hydrogen bonds : bond 0.05390 ( 1139) hydrogen bonds : angle 5.20762 ( 3177) metal coordination : bond 0.06192 ( 36) metal coordination : angle 8.65796 ( 81) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 411 time to evaluate : 1.218 Fit side-chains REVERT: A 178 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 268 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 457 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.6445 (m90) REVERT: E 49 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8540 (tp) REVERT: E 100 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8037 (ttm-80) REVERT: E 116 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (t) REVERT: G 84 LEU cc_start: 0.8154 (mm) cc_final: 0.7904 (mm) REVERT: G 92 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7104 (mttt) REVERT: G 122 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6882 (mmt) REVERT: G 139 MET cc_start: 0.7570 (mmp) cc_final: 0.7280 (mmm) REVERT: G 142 GLN cc_start: 0.7699 (tp40) cc_final: 0.7129 (tp40) REVERT: J 162 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: J 291 TYR cc_start: 0.8084 (p90) cc_final: 0.7852 (p90) REVERT: J 303 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6679 (tpt90) REVERT: J 313 TRP cc_start: 0.6442 (m-90) cc_final: 0.6095 (m-10) REVERT: K 85 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7996 (p) REVERT: L 86 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9099 (t0) REVERT: M 467 LYS cc_start: 0.8199 (tttm) cc_final: 0.7899 (tttm) REVERT: M 535 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: N 9 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5552 (mtm-85) REVERT: Q 104 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7329 (tp30) outliers start: 89 outliers final: 35 residues processed: 465 average time/residue: 0.8835 time to fit residues: 467.1190 Evaluate side-chains 446 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 399 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 441 HIS H 71 GLN J 79 GLN K 77 GLN M 39 GLN M 51 GLN M 464 GLN O 131 HIS O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN Q 149 GLN Q 182 ASN Q 285 ASN T 43 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100661 restraints weight = 30414.378| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.16 r_work: 0.2953 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.471 29034 Z= 0.240 Angle : 0.775 29.234 39372 Z= 0.357 Chirality : 0.049 0.218 4259 Planarity : 0.006 0.084 5054 Dihedral : 11.217 177.917 4155 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.31 % Allowed : 13.75 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.14), residues: 3477 helix: 0.95 (0.14), residues: 1360 sheet: 0.11 (0.26), residues: 344 loop : -0.37 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 138 TYR 0.025 0.002 TYR J 180 PHE 0.024 0.002 PHE L 164 TRP 0.015 0.002 TRP M 422 HIS 0.007 0.002 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00553 (28995) covalent geometry : angle 0.67453 (39289) SS BOND : bond 0.01381 ( 1) SS BOND : angle 3.90284 ( 2) hydrogen bonds : bond 0.06233 ( 1139) hydrogen bonds : angle 5.28563 ( 3177) metal coordination : bond 0.08020 ( 36) metal coordination : angle 8.42817 ( 81) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 395 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 178 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: E 42 GLU cc_start: 0.8632 (tp30) cc_final: 0.8430 (tp30) REVERT: E 49 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 100 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8096 (ttm-80) REVERT: E 116 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8155 (t) REVERT: F 43 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7491 (mm-30) REVERT: G 84 LEU cc_start: 0.8228 (mm) cc_final: 0.7940 (mm) REVERT: G 87 LEU cc_start: 0.7813 (mt) cc_final: 0.7551 (tp) REVERT: G 92 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7186 (mttp) REVERT: G 142 GLN cc_start: 0.7792 (tp40) cc_final: 0.7160 (tp40) REVERT: J 85 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8840 (ppt170) REVERT: J 162 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: J 189 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8381 (mptm) REVERT: J 303 ARG cc_start: 0.7048 (ttp80) cc_final: 0.6641 (tpt90) REVERT: J 313 TRP cc_start: 0.6426 (m-90) cc_final: 0.6034 (m-10) REVERT: K 85 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8038 (p) REVERT: M 467 LYS cc_start: 0.8227 (tttm) cc_final: 0.7902 (tttp) REVERT: M 535 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: M 688 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7951 (mt0) REVERT: N 9 ARG cc_start: 0.5912 (mtm-85) cc_final: 0.5471 (mtm-85) REVERT: O 154 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (tttm) REVERT: O 172 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8241 (pt) REVERT: Q 104 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7380 (tp30) outliers start: 100 outliers final: 49 residues processed: 463 average time/residue: 0.8763 time to fit residues: 460.4116 Evaluate side-chains 452 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 388 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 535 GLU 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 688 GLN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 240 optimal weight: 9.9990 chunk 273 optimal weight: 0.0870 chunk 334 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS F 48 ASN H 71 GLN K 77 GLN M 39 GLN M 464 GLN M 678 GLN O 153 GLN P 236 ASN T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105592 restraints weight = 30485.919| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.20 r_work: 0.3015 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.220 29034 Z= 0.116 Angle : 0.676 39.831 39372 Z= 0.278 Chirality : 0.042 0.152 4259 Planarity : 0.005 0.076 5054 Dihedral : 10.273 178.666 4151 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 2.78 % Allowed : 14.55 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3477 helix: 1.25 (0.14), residues: 1353 sheet: 0.00 (0.25), residues: 370 loop : -0.28 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 179 TYR 0.015 0.001 TYR P 64 PHE 0.016 0.001 PHE L 164 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00242 (28995) covalent geometry : angle 0.52209 (39289) SS BOND : bond 0.00859 ( 1) SS BOND : angle 2.91272 ( 2) hydrogen bonds : bond 0.04299 ( 1139) hydrogen bonds : angle 4.89695 ( 3177) metal coordination : bond 0.03785 ( 36) metal coordination : angle 9.46354 ( 81) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 404 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6957 (mtpm) REVERT: A 132 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7528 (ptp-170) REVERT: A 178 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: C 99 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: E 49 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (tp) REVERT: E 100 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8518 (ttm110) REVERT: E 116 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (t) REVERT: F 89 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7531 (mtp180) REVERT: F 92 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7469 (pt0) REVERT: G 84 LEU cc_start: 0.8207 (mm) cc_final: 0.7908 (mm) REVERT: G 139 MET cc_start: 0.7617 (mmp) cc_final: 0.7312 (mmm) REVERT: G 142 GLN cc_start: 0.7734 (tp40) cc_final: 0.7065 (tp40) REVERT: J 189 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8302 (mptm) REVERT: J 254 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8040 (mptm) REVERT: J 303 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6585 (tpt90) REVERT: J 313 TRP cc_start: 0.6394 (m-90) cc_final: 0.6016 (m-10) REVERT: K 85 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7989 (p) REVERT: M 688 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: N 9 ARG cc_start: 0.5927 (mtm-85) cc_final: 0.5498 (mtm-85) REVERT: O 202 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: Q 104 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: Q 149 GLN cc_start: 0.9048 (tt0) cc_final: 0.8805 (tt0) outliers start: 84 outliers final: 31 residues processed: 465 average time/residue: 0.8479 time to fit residues: 448.0282 Evaluate side-chains 433 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 166 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 328 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 277 ASN A 344 GLN A 376 HIS H 71 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN O 153 GLN O 246 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN T 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100317 restraints weight = 30299.294| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.15 r_work: 0.2947 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.462 29034 Z= 0.238 Angle : 0.764 29.546 39372 Z= 0.350 Chirality : 0.049 0.226 4259 Planarity : 0.006 0.080 5054 Dihedral : 10.429 174.313 4144 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.47 % Allowed : 14.84 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3477 helix: 1.03 (0.14), residues: 1358 sheet: 0.15 (0.26), residues: 333 loop : -0.42 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 138 TYR 0.024 0.002 TYR J 180 PHE 0.023 0.002 PHE L 164 TRP 0.014 0.002 TRP M 422 HIS 0.007 0.002 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00554 (28995) covalent geometry : angle 0.66168 (39289) SS BOND : bond 0.01372 ( 1) SS BOND : angle 3.85163 ( 2) hydrogen bonds : bond 0.06030 ( 1139) hydrogen bonds : angle 5.19034 ( 3177) metal coordination : bond 0.07864 ( 36) metal coordination : angle 8.43374 ( 81) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 394 time to evaluate : 1.148 Fit side-chains REVERT: A 36 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6976 (mtpm) REVERT: A 132 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7668 (ptp-170) REVERT: A 178 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 268 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 99 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: E 49 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (tp) REVERT: E 100 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8044 (ttm-80) REVERT: E 116 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (t) REVERT: F 92 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7542 (pt0) REVERT: G 84 LEU cc_start: 0.8238 (mm) cc_final: 0.7879 (mm) REVERT: G 92 LYS cc_start: 0.7435 (mtpp) cc_final: 0.7126 (mttt) REVERT: G 142 GLN cc_start: 0.7786 (tp40) cc_final: 0.7013 (tp40) REVERT: J 85 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8867 (ppt170) REVERT: J 254 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8140 (mptm) REVERT: J 303 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6571 (tmt90) REVERT: J 310 PHE cc_start: 0.7788 (m-80) cc_final: 0.7346 (m-10) REVERT: J 313 TRP cc_start: 0.6371 (m-90) cc_final: 0.6004 (m-10) REVERT: K 85 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8010 (p) REVERT: M 54 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: M 467 LYS cc_start: 0.8228 (tttm) cc_final: 0.7910 (tttp) REVERT: M 470 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8169 (mmtm) REVERT: M 535 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: M 688 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: N 9 ARG cc_start: 0.5924 (mtm-85) cc_final: 0.5486 (mtm-85) REVERT: O 154 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8129 (tttm) REVERT: O 205 ILE cc_start: 0.8489 (mm) cc_final: 0.8266 (mt) REVERT: Q 104 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: T 104 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7341 (tppp) outliers start: 105 outliers final: 50 residues processed: 464 average time/residue: 0.8337 time to fit residues: 440.4312 Evaluate side-chains 462 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 394 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 535 GLU 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 688 GLN Chi-restraints excluded: chain M residue 714 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 323 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 344 GLN H 71 GLN J 154 GLN K 77 GLN M 39 GLN M 464 GLN M 678 GLN O 153 GLN P 236 ASN Q 149 GLN T 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105164 restraints weight = 30485.632| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.17 r_work: 0.3031 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 29034 Z= 0.114 Angle : 0.679 41.334 39372 Z= 0.277 Chirality : 0.042 0.149 4259 Planarity : 0.005 0.076 5054 Dihedral : 9.752 175.156 4144 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 2.55 % Allowed : 15.70 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3477 helix: 1.28 (0.14), residues: 1359 sheet: -0.00 (0.25), residues: 363 loop : -0.30 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 179 TYR 0.015 0.001 TYR P 64 PHE 0.016 0.001 PHE L 164 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00238 (28995) covalent geometry : angle 0.52155 (39289) SS BOND : bond 0.00841 ( 1) SS BOND : angle 2.94878 ( 2) hydrogen bonds : bond 0.04189 ( 1139) hydrogen bonds : angle 4.83744 ( 3177) metal coordination : bond 0.03665 ( 36) metal coordination : angle 9.58911 ( 81) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 1.188 Fit side-chains REVERT: A 36 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6912 (mtpm) REVERT: A 132 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: A 178 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: A 268 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: A 451 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: C 99 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: E 49 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8503 (tp) REVERT: E 100 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8470 (ttm110) REVERT: E 116 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8205 (t) REVERT: F 89 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7528 (mtp180) REVERT: F 92 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7471 (pt0) REVERT: G 84 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7856 (mm) REVERT: G 92 LYS cc_start: 0.7405 (mtpp) cc_final: 0.7144 (mttt) REVERT: G 105 MET cc_start: 0.7367 (mpt) cc_final: 0.7093 (mpt) REVERT: G 122 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.6489 (mmt) REVERT: G 139 MET cc_start: 0.7547 (mmp) cc_final: 0.7201 (mmm) REVERT: G 142 GLN cc_start: 0.7732 (tp40) cc_final: 0.6918 (tp40) REVERT: H 67 LYS cc_start: 0.8198 (mttm) cc_final: 0.7982 (mttm) REVERT: J 254 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8030 (mptm) REVERT: J 303 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6645 (tpt90) REVERT: J 310 PHE cc_start: 0.7640 (m-80) cc_final: 0.7187 (m-10) REVERT: J 313 TRP cc_start: 0.6329 (m-90) cc_final: 0.5955 (m-10) REVERT: M 688 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: N 9 ARG cc_start: 0.5896 (mtm-85) cc_final: 0.5429 (mtm-85) REVERT: Q 149 GLN cc_start: 0.9035 (tt0) cc_final: 0.8797 (tt0) REVERT: Q 274 ASP cc_start: 0.8822 (m-30) cc_final: 0.8581 (m-30) outliers start: 77 outliers final: 32 residues processed: 464 average time/residue: 0.8602 time to fit residues: 455.1955 Evaluate side-chains 439 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 394 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 235 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 308 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS F 62 GLN H 71 GLN J 154 GLN K 77 GLN M 39 GLN O 153 GLN P 236 ASN T 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103682 restraints weight = 30437.883| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.23 r_work: 0.2992 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.307 29034 Z= 0.143 Angle : 0.687 35.295 39372 Z= 0.294 Chirality : 0.044 0.162 4259 Planarity : 0.005 0.074 5054 Dihedral : 9.672 175.001 4144 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.81 % Allowed : 15.67 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3477 helix: 1.32 (0.14), residues: 1358 sheet: 0.08 (0.25), residues: 358 loop : -0.31 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 179 TYR 0.017 0.002 TYR J 180 PHE 0.019 0.001 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00316 (28995) covalent geometry : angle 0.55706 (39289) SS BOND : bond 0.01001 ( 1) SS BOND : angle 3.12069 ( 2) hydrogen bonds : bond 0.04639 ( 1139) hydrogen bonds : angle 4.86988 ( 3177) metal coordination : bond 0.05243 ( 36) metal coordination : angle 8.88039 ( 81) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 401 time to evaluate : 1.344 Fit side-chains REVERT: A 36 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6927 (mtpm) REVERT: A 132 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7644 (ptp-170) REVERT: A 178 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: A 268 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: A 451 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: A 457 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6327 (m90) REVERT: C 99 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: E 49 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 100 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8528 (ttm110) REVERT: E 116 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8215 (t) REVERT: F 89 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7553 (mtp180) REVERT: F 92 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7504 (pt0) REVERT: G 84 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7859 (mm) REVERT: G 92 LYS cc_start: 0.7401 (mtpp) cc_final: 0.7113 (mttt) REVERT: G 122 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6752 (mmt) REVERT: G 139 MET cc_start: 0.7595 (mmp) cc_final: 0.7255 (mmm) REVERT: G 142 GLN cc_start: 0.7756 (tp40) cc_final: 0.7011 (tp40) REVERT: J 254 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8088 (mptm) REVERT: J 303 ARG cc_start: 0.7010 (ttp80) cc_final: 0.6642 (tpt90) REVERT: J 310 PHE cc_start: 0.7728 (m-80) cc_final: 0.7276 (m-10) REVERT: J 313 TRP cc_start: 0.6382 (m-90) cc_final: 0.5995 (m-10) REVERT: K 85 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7965 (p) REVERT: M 54 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: N 9 ARG cc_start: 0.5832 (mtm-85) cc_final: 0.5445 (mtm-85) REVERT: Q 149 GLN cc_start: 0.9077 (tt0) cc_final: 0.8804 (tt0) outliers start: 85 outliers final: 46 residues processed: 461 average time/residue: 0.8484 time to fit residues: 447.0102 Evaluate side-chains 452 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 391 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 714 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 72 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 328 optimal weight: 2.9990 chunk 275 optimal weight: 0.0770 chunk 325 optimal weight: 0.0050 chunk 332 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 169 optimal weight: 0.1980 overall best weight: 0.6732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 456 GLN F 62 GLN H 71 GLN J 154 GLN K 77 GLN M 39 GLN M 359 ASN M 464 GLN O 153 GLN P 236 ASN T 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106623 restraints weight = 30559.373| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.17 r_work: 0.3054 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.200 29034 Z= 0.108 Angle : 0.668 40.562 39372 Z= 0.269 Chirality : 0.042 0.147 4259 Planarity : 0.004 0.073 5054 Dihedral : 9.221 176.262 4144 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.68 % Allowed : 15.77 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3477 helix: 1.44 (0.14), residues: 1361 sheet: 0.01 (0.25), residues: 399 loop : -0.20 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 179 TYR 0.014 0.001 TYR P 64 PHE 0.016 0.001 PHE L 164 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00232 (28995) covalent geometry : angle 0.51198 (39289) SS BOND : bond 0.00781 ( 1) SS BOND : angle 2.87021 ( 2) hydrogen bonds : bond 0.03856 ( 1139) hydrogen bonds : angle 4.67164 ( 3177) metal coordination : bond 0.03449 ( 36) metal coordination : angle 9.47646 ( 81) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 1.184 Fit side-chains REVERT: A 36 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6862 (mtpm) REVERT: A 132 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7517 (ptp-170) REVERT: A 178 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: A 268 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 451 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: C 99 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: E 23 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7538 (mtp180) REVERT: E 49 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (tp) REVERT: E 69 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8250 (tptt) REVERT: E 99 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: E 100 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (ttm110) REVERT: F 43 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7242 (mt-10) REVERT: F 89 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7509 (mtp180) REVERT: F 92 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7478 (pt0) REVERT: G 84 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7837 (mm) REVERT: G 92 LYS cc_start: 0.7305 (mtpp) cc_final: 0.7069 (mttt) REVERT: G 122 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.6410 (mmt) REVERT: G 139 MET cc_start: 0.7597 (mmp) cc_final: 0.7174 (mmm) REVERT: G 142 GLN cc_start: 0.7719 (tp40) cc_final: 0.6946 (tp40) REVERT: I 70 MET cc_start: 0.7982 (tmt) cc_final: 0.7772 (tmt) REVERT: J 254 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8025 (mptm) REVERT: J 303 ARG cc_start: 0.6941 (ttp80) cc_final: 0.6562 (tpt90) REVERT: J 310 PHE cc_start: 0.7600 (m-80) cc_final: 0.7144 (m-10) REVERT: J 313 TRP cc_start: 0.6365 (m-90) cc_final: 0.6015 (m-10) REVERT: K 85 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7933 (p) REVERT: N 9 ARG cc_start: 0.5897 (mtm-85) cc_final: 0.5429 (mtm-85) REVERT: P 240 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (pp20) REVERT: Q 97 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8592 (mp) REVERT: Q 104 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: Q 149 GLN cc_start: 0.9026 (tt0) cc_final: 0.8762 (tt0) REVERT: T 104 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7339 (tppp) outliers start: 81 outliers final: 36 residues processed: 463 average time/residue: 0.8330 time to fit residues: 441.9928 Evaluate side-chains 447 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 394 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 44 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 149 optimal weight: 0.3980 chunk 193 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 256 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 344 GLN J 38 HIS J 154 GLN K 77 GLN M 39 GLN M 359 ASN O 153 GLN O 246 GLN P 236 ASN T 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105122 restraints weight = 30519.911| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.19 r_work: 0.3018 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.275 29034 Z= 0.128 Angle : 0.675 36.112 39372 Z= 0.284 Chirality : 0.043 0.154 4259 Planarity : 0.005 0.068 5054 Dihedral : 9.183 176.247 4143 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.31 % Allowed : 16.23 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3477 helix: 1.42 (0.14), residues: 1366 sheet: 0.06 (0.25), residues: 378 loop : -0.18 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 191 TYR 0.015 0.001 TYR J 180 PHE 0.017 0.001 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00278 (28995) covalent geometry : angle 0.54073 (39289) SS BOND : bond 0.00899 ( 1) SS BOND : angle 2.96759 ( 2) hydrogen bonds : bond 0.04292 ( 1139) hydrogen bonds : angle 4.73113 ( 3177) metal coordination : bond 0.04681 ( 36) metal coordination : angle 8.92010 ( 81) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 400 time to evaluate : 1.181 Fit side-chains REVERT: A 36 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6871 (mtpm) REVERT: A 132 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7591 (ptp-170) REVERT: A 178 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: A 268 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 451 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: C 99 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: E 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 69 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8297 (tptt) REVERT: E 99 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: E 100 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8506 (ttm110) REVERT: F 43 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7287 (mt-10) REVERT: F 89 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7540 (mtp180) REVERT: F 92 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7502 (pt0) REVERT: G 84 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7830 (mm) REVERT: G 122 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6725 (mmt) REVERT: G 139 MET cc_start: 0.7594 (mmp) cc_final: 0.7206 (mmm) REVERT: G 142 GLN cc_start: 0.7730 (tp40) cc_final: 0.6919 (tp40) REVERT: I 70 MET cc_start: 0.8089 (tmt) cc_final: 0.7842 (tmt) REVERT: J 254 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8064 (mptm) REVERT: J 303 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6582 (tpt90) REVERT: J 310 PHE cc_start: 0.7700 (m-80) cc_final: 0.7238 (m-10) REVERT: J 313 TRP cc_start: 0.6350 (m-90) cc_final: 0.5999 (m-10) REVERT: K 85 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (p) REVERT: L 76 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8982 (tptm) REVERT: N 9 ARG cc_start: 0.5804 (mtm-85) cc_final: 0.5389 (mtm-85) REVERT: Q 97 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8614 (mp) REVERT: Q 104 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: Q 149 GLN cc_start: 0.9050 (tt0) cc_final: 0.8785 (tt0) REVERT: T 104 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7334 (tppp) outliers start: 70 outliers final: 40 residues processed: 451 average time/residue: 0.8430 time to fit residues: 435.1172 Evaluate side-chains 452 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 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 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 112 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 344 GLN A 376 HIS ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN J 154 GLN K 77 GLN M 39 GLN O 153 GLN P 236 ASN T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.102783 restraints weight = 30284.976| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.19 r_work: 0.2984 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.357 29034 Z= 0.173 Angle : 0.715 33.392 39372 Z= 0.314 Chirality : 0.045 0.177 4259 Planarity : 0.005 0.069 5054 Dihedral : 9.370 174.647 4143 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.41 % Allowed : 16.30 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3477 helix: 1.33 (0.14), residues: 1359 sheet: 0.11 (0.26), residues: 343 loop : -0.27 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 191 TYR 0.020 0.002 TYR J 180 PHE 0.019 0.002 PHE L 164 TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00393 (28995) covalent geometry : angle 0.59719 (39289) SS BOND : bond 0.01094 ( 1) SS BOND : angle 3.22864 ( 2) hydrogen bonds : bond 0.05033 ( 1139) hydrogen bonds : angle 4.90113 ( 3177) metal coordination : bond 0.06076 ( 36) metal coordination : angle 8.65468 ( 81) Misc. bond : bond 0.00083 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 396 time to evaluate : 1.177 Fit side-chains REVERT: A 36 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6876 (mtpm) REVERT: A 132 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7596 (ptp-170) REVERT: A 178 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: A 268 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: C 99 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: E 49 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (tp) REVERT: E 99 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: E 100 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8518 (ttm110) REVERT: F 43 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7301 (mt-10) REVERT: G 84 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7821 (mm) REVERT: G 92 LYS cc_start: 0.7363 (mtpp) cc_final: 0.6996 (mttt) REVERT: G 139 MET cc_start: 0.7606 (mmp) cc_final: 0.7233 (mmm) REVERT: G 142 GLN cc_start: 0.7751 (tp40) cc_final: 0.6920 (tp40) REVERT: J 254 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8108 (mptm) REVERT: J 303 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6563 (tpt90) REVERT: J 310 PHE cc_start: 0.7749 (m-80) cc_final: 0.7292 (m-10) REVERT: J 313 TRP cc_start: 0.6366 (m-90) cc_final: 0.6021 (m-10) REVERT: K 85 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7966 (p) REVERT: L 76 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8995 (tptm) REVERT: M 54 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: M 535 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: N 9 ARG cc_start: 0.5812 (mtm-85) cc_final: 0.5447 (mtm-85) REVERT: Q 97 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8637 (mp) REVERT: Q 104 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: T 104 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7367 (tppp) outliers start: 73 outliers final: 45 residues processed: 451 average time/residue: 0.8232 time to fit residues: 424.2556 Evaluate side-chains 456 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 394 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 254 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 539 LYS 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 714 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 291 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 74 optimal weight: 3.9990 chunk 255 optimal weight: 0.0040 chunk 283 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 344 GLN A 376 HIS ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN J 154 GLN K 77 GLN M 39 GLN M 359 ASN M 464 GLN O 153 GLN P 236 ASN Q 149 GLN T 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105840 restraints weight = 30646.724| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.20 r_work: 0.3032 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.230 29034 Z= 0.116 Angle : 0.678 39.279 39372 Z= 0.279 Chirality : 0.042 0.146 4259 Planarity : 0.004 0.069 5054 Dihedral : 9.072 175.120 4143 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.25 % Allowed : 16.46 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3477 helix: 1.41 (0.14), residues: 1366 sheet: -0.02 (0.25), residues: 392 loop : -0.17 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 191 TYR 0.015 0.001 TYR J 180 PHE 0.017 0.001 PHE L 164 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00249 (28995) covalent geometry : angle 0.53222 (39289) SS BOND : bond 0.00800 ( 1) SS BOND : angle 2.91816 ( 2) hydrogen bonds : bond 0.04103 ( 1139) hydrogen bonds : angle 4.71687 ( 3177) metal coordination : bond 0.03943 ( 36) metal coordination : angle 9.28223 ( 81) Misc. bond : bond 0.00051 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13632.63 seconds wall clock time: 232 minutes 17.45 seconds (13937.45 seconds total)