Starting phenix.real_space_refine on Fri Mar 6 22:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nyv_12655/03_2026/7nyv_12655.map" } resolution = 3.7 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= 0.001 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 1 5.49 5 S 243 5.16 5 C 22719 2.51 5 N 5962 2.21 5 O 6270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 35228 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1222 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4725 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3424 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 7044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7044 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "I" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 144} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 668 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1985 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TRP:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 21, 'TRANS': 482} Chain: "L" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4126 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 18, 'TRANS': 593} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'HIS:plan': 8, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 5, 'PHE:plan': 11, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 3, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 268 Chain: "N" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3543 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 810 SG CYS B 158 176.673 109.535 71.531 1.00 70.15 S ATOM 181 SG CYS B 64 174.302 103.600 71.206 1.00 92.83 S ATOM 175 SG CYS B 63 171.053 106.727 68.030 1.00 97.83 S ATOM 593 SG CYS B 129 171.469 109.724 73.377 1.00 67.58 S ATOM 6594 SG CYS E 92 224.613 164.830 67.842 1.00 62.87 S ATOM 6628 SG CYS E 97 227.316 164.614 66.047 1.00 69.61 S ATOM 6907 SG CYS E 133 221.704 168.480 66.062 1.00 63.52 S ATOM 6933 SG CYS E 137 223.508 169.129 64.342 1.00 67.90 S ATOM 9934 SG CYS F 357 204.884 159.479 67.080 1.00 47.47 S ATOM 9914 SG CYS F 354 200.223 159.714 68.042 1.00 48.35 S ATOM 10255 SG CYS F 398 202.825 165.207 66.923 1.00 45.59 S ATOM 9890 SG CYS F 351 203.245 162.718 72.597 1.00 47.04 S ATOM 10951 SG CYS G 48 187.375 157.819 67.040 1.00 45.65 S ATOM 11100 SG CYS G 67 187.745 160.399 69.592 1.00 43.17 S ATOM 10849 SG CYS G 34 189.980 158.082 72.639 1.00 49.82 S ATOM 10925 SG CYS G 45 190.966 155.233 70.663 1.00 45.41 S ATOM 11831 SG CYS G 157 195.183 154.643 83.799 1.00 40.35 S ATOM 11783 SG CYS G 151 198.488 151.005 79.916 1.00 44.33 S ATOM 11802 SG CYS G 154 192.578 153.093 78.372 1.00 49.00 S ATOM 12179 SG CYS G 201 192.507 148.908 82.598 1.00 39.75 S ATOM 11408 SG CYS G 106 193.241 139.839 81.848 1.00 40.86 S ATOM 11388 SG CYS G 103 194.041 137.198 75.907 1.00 57.52 S ATOM 11448 SG CYS G 112 190.243 142.676 77.499 1.00 40.82 S ATOM 12428 SG CYS G 231 174.947 154.632 100.969 1.00 49.12 S ATOM 12452 SG CYS G 235 175.487 153.642 95.435 1.00 42.65 S ATOM 12689 SG CYS G 263 179.308 152.819 97.857 1.00 57.31 S ATOM 12404 SG CYS G 228 175.598 150.092 98.316 1.00 45.04 S ATOM 12452 SG CYS G 235 175.487 153.642 95.435 1.00 42.65 S ATOM 12404 SG CYS G 228 175.598 150.092 98.316 1.00 45.04 S ATOM 12689 SG CYS G 263 179.308 152.819 97.857 1.00 57.31 S ATOM 18292 SG CYS I 109 193.129 123.215 77.714 1.00 48.64 S ATOM 17915 SG CYS I 60 192.783 123.131 84.331 1.00 48.98 S ATOM 17955 SG CYS I 66 187.647 122.689 80.597 1.00 46.59 S ATOM 17933 SG CYS I 63 190.911 127.536 79.690 1.00 48.39 S ATOM 17978 SG CYS I 70 180.389 119.358 77.416 1.00 52.21 S ATOM 18245 SG CYS I 102 181.972 117.249 72.525 1.00 53.20 S ATOM 18220 SG CYS I 99 182.436 112.975 77.592 1.00 59.90 S ATOM 18263 SG CYS I 105 186.401 117.868 75.896 1.00 56.35 S Time building chain proxies: 7.98, per 1000 atoms: 0.23 Number of scatterers: 35228 At special positions: 0 Unit cell: (254.43, 214.338, 143.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 243 16.00 P 1 15.00 O 6270 8.00 N 5962 7.00 C 22719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " Number of angles added : 93 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 25 sheets defined 60.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 76 removed outlier: 4.038A pdb=" N MET B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.529A pdb=" N ILE B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.616A pdb=" N LYS B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.675A pdb=" N LYS B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.543A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 52 through 63 Processing helix chain 'D' and resid 129 through 141 removed outlier: 4.118A pdb=" N TYR D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.621A pdb=" N LYS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.784A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.527A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 269' Processing helix chain 'D' and resid 276 through 292 removed outlier: 3.522A pdb=" N GLU D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 296 through 326 removed outlier: 3.572A pdb=" N ASN D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.895A pdb=" N THR D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 396 removed outlier: 3.746A pdb=" N LEU D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.569A pdb=" N ASN D 445 " --> pdb=" O GLY D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 483 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 507 through 520 Processing helix chain 'D' and resid 559 through 572 removed outlier: 4.398A pdb=" N ALA D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Proline residue: D 569 - end of helix Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 590 through 596 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 52 through 63 removed outlier: 4.163A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.530A pdb=" N VAL E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.058A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.723A pdb=" N TYR E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.547A pdb=" N GLY F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 75 removed outlier: 3.512A pdb=" N LYS F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.160A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.848A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.836A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 4.051A pdb=" N ASN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.624A pdb=" N ILE F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 374 removed outlier: 3.758A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.539A pdb=" N GLY F 403 " --> pdb=" O ALA F 399 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.832A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 81 through 97 Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 148 through 151 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 175 through 179 removed outlier: 3.983A pdb=" N VAL G 179 " --> pdb=" O HIS G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 201 Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.640A pdb=" N GLU G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 214' Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 263 through 269 Processing helix chain 'G' and resid 270 through 275 removed outlier: 3.538A pdb=" N LEU G 275 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 309 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 342 through 359 Processing helix chain 'G' and resid 367 through 372 Processing helix chain 'G' and resid 386 through 398 removed outlier: 3.617A pdb=" N ALA G 390 " --> pdb=" O GLY G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 408 Processing helix chain 'G' and resid 414 through 423 removed outlier: 3.536A pdb=" N GLN G 423 " --> pdb=" O LEU G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 466 Processing helix chain 'G' and resid 476 through 492 Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'G' and resid 506 through 523 removed outlier: 3.911A pdb=" N ILE G 510 " --> pdb=" O SER G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 545 Processing helix chain 'G' and resid 548 through 558 Processing helix chain 'G' and resid 576 through 586 Processing helix chain 'G' and resid 598 through 602 removed outlier: 3.671A pdb=" N GLU G 602 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 616 removed outlier: 3.553A pdb=" N SER G 616 " --> pdb=" O PHE G 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 662 Processing helix chain 'G' and resid 668 through 680 Processing helix chain 'G' and resid 681 through 689 removed outlier: 5.222A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 769 removed outlier: 3.764A pdb=" N GLN G 769 " --> pdb=" O ASN G 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 824 through 832 Proline residue: G 829 - end of helix Processing helix chain 'G' and resid 843 through 851 Processing helix chain 'G' and resid 892 through 896 Processing helix chain 'I' and resid 24 through 29 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.699A pdb=" N VAL I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.509A pdb=" N GLU I 107 " --> pdb=" O GLY I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'K' and resid 3 through 25 removed outlier: 4.186A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 53 removed outlier: 3.931A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.625A pdb=" N TYR K 62 " --> pdb=" O GLY K 58 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 24 through 47 removed outlier: 3.606A pdb=" N ALA J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 removed outlier: 4.096A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 removed outlier: 3.925A pdb=" N ASN J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'J' and resid 89 through 113 removed outlier: 3.714A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.859A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 133 removed outlier: 4.069A pdb=" N VAL J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 159 removed outlier: 3.592A pdb=" N VAL J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 38 Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.726A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 120 Processing helix chain 'H' and resid 56 through 68 removed outlier: 4.447A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 97 Proline residue: H 87 - end of helix removed outlier: 3.665A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 removed outlier: 3.766A pdb=" N VAL H 101 " --> pdb=" O PHE H 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 98 through 101' Processing helix chain 'H' and resid 115 through 138 removed outlier: 4.359A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 Processing helix chain 'H' and resid 158 through 172 removed outlier: 4.264A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.587A pdb=" N ILE H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 206 Processing helix chain 'H' and resid 231 through 256 removed outlier: 4.343A pdb=" N GLY H 235 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 289 Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 304 through 321 removed outlier: 3.689A pdb=" N LEU H 308 " --> pdb=" O ILE H 304 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU H 321 " --> pdb=" O ALA H 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 26 through 50 removed outlier: 4.168A pdb=" N TRP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE M 34 " --> pdb=" O TRP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 135 through 146 Processing helix chain 'M' and resid 148 through 159 removed outlier: 3.804A pdb=" N PHE M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 167 removed outlier: 3.883A pdb=" N THR M 166 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 167 " --> pdb=" O GLY M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 163 through 167' Processing helix chain 'M' and resid 169 through 200 removed outlier: 3.822A pdb=" N THR M 178 " --> pdb=" O PHE M 174 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 219 through 231 removed outlier: 3.764A pdb=" N LEU M 223 " --> pdb=" O VAL M 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 251 removed outlier: 4.470A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 262 removed outlier: 3.781A pdb=" N ILE M 262 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 274 removed outlier: 4.435A pdb=" N ALA M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 331 removed outlier: 3.986A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 removed outlier: 3.515A pdb=" N TYR M 338 " --> pdb=" O SER M 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU M 355 " --> pdb=" O SER M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 396 removed outlier: 3.986A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 418 removed outlier: 4.130A pdb=" N VAL M 405 " --> pdb=" O THR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 426 removed outlier: 4.095A pdb=" N THR M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 444 Processing helix chain 'M' and resid 447 through 456 removed outlier: 3.752A pdb=" N GLN M 451 " --> pdb=" O ALA M 448 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE M 452 " --> pdb=" O LYS M 449 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA M 453 " --> pdb=" O SER M 450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU M 456 " --> pdb=" O ALA M 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 removed outlier: 3.626A pdb=" N LEU M 465 " --> pdb=" O SER M 461 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU M 471 " --> pdb=" O MET M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 482 through 503 removed outlier: 5.120A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 removed outlier: 3.652A pdb=" N LEU L 10 " --> pdb=" O LEU L 6 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 26 through 55 removed outlier: 3.612A pdb=" N SER L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.677A pdb=" N VAL L 92 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 removed outlier: 3.802A pdb=" N ASN L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 155 Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.575A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA L 167 " --> pdb=" O ASN L 163 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA L 184 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 202 Processing helix chain 'L' and resid 203 through 208 Processing helix chain 'L' and resid 212 through 230 removed outlier: 4.031A pdb=" N MET L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 236 Processing helix chain 'L' and resid 240 through 245 removed outlier: 3.824A pdb=" N GLY L 245 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 255 Processing helix chain 'L' and resid 261 through 269 removed outlier: 3.565A pdb=" N ILE L 266 " --> pdb=" O GLY L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 275 Processing helix chain 'L' and resid 276 through 295 removed outlier: 3.549A pdb=" N LEU L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL L 283 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU L 292 " --> pdb=" O ALA L 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY L 295 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.981A pdb=" N GLN L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 357 removed outlier: 4.079A pdb=" N PHE L 340 " --> pdb=" O MET L 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 344 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS L 357 " --> pdb=" O ILE L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 removed outlier: 4.021A pdb=" N TYR L 376 " --> pdb=" O ILE L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 410 Processing helix chain 'L' and resid 411 through 437 removed outlier: 4.349A pdb=" N PHE L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG L 431 " --> pdb=" O LEU L 427 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 465 Proline residue: L 456 - end of helix removed outlier: 3.700A pdb=" N THR L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 470 removed outlier: 3.675A pdb=" N ALA L 469 " --> pdb=" O THR L 465 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 465 through 470' Processing helix chain 'L' and resid 489 through 514 Processing helix chain 'L' and resid 516 through 523 Processing helix chain 'L' and resid 525 through 537 Processing helix chain 'L' and resid 540 through 548 Processing helix chain 'L' and resid 549 through 560 Processing helix chain 'L' and resid 563 through 569 removed outlier: 3.658A pdb=" N SER L 567 " --> pdb=" O ASP L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 570 through 587 removed outlier: 3.522A pdb=" N GLU L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 611 removed outlier: 3.643A pdb=" N TYR L 594 " --> pdb=" O TYR L 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 11 Processing helix chain 'N' and resid 11 through 31 removed outlier: 3.591A pdb=" N GLY N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 58 removed outlier: 4.105A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 96 removed outlier: 3.539A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 120 removed outlier: 4.337A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 142 removed outlier: 3.576A pdb=" N PHE N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 179 removed outlier: 3.698A pdb=" N TYR N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 216 Processing helix chain 'N' and resid 220 through 224 removed outlier: 3.971A pdb=" N HIS N 224 " --> pdb=" O VAL N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 234 removed outlier: 4.455A pdb=" N ASP N 229 " --> pdb=" O LEU N 225 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 244 removed outlier: 3.613A pdb=" N PHE N 241 " --> pdb=" O PRO N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 261 removed outlier: 3.676A pdb=" N GLY N 252 " --> pdb=" O ILE N 248 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL N 253 " --> pdb=" O ALA N 249 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE N 258 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 286 removed outlier: 3.654A pdb=" N ARG N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 314 removed outlier: 3.826A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.731A pdb=" N SER N 348 " --> pdb=" O VAL N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 385 removed outlier: 3.847A pdb=" N ALA N 384 " --> pdb=" O MET N 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY N 385 " --> pdb=" O LEU N 381 " (cutoff:3.500A) Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.926A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 432 removed outlier: 4.654A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR N 425 " --> pdb=" O GLY N 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 470 Processing helix chain 'N' and resid 471 through 482 removed outlier: 3.550A pdb=" N ILE N 475 " --> pdb=" O PRO N 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.593A pdb=" N PHE B 59 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 99 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.887A pdb=" N THR D 35 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP D 47 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.902A pdb=" N VAL D 120 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 146 " --> pdb=" O VAL D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 212 through 214 removed outlier: 4.114A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 360 Processing sheet with id=AA6, first strand: chain 'D' and resid 528 through 534 Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.640A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 168 through 173 removed outlier: 3.585A pdb=" N HIS F 172 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 132 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 87 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE F 131 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS F 89 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CSX F 215 " --> pdb=" O TYR F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 265 removed outlier: 7.528A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 13 removed outlier: 7.340A pdb=" N THR G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ILE G 77 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N HIS G 5 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB4, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AB5, first strand: chain 'G' and resid 222 through 223 removed outlier: 8.420A pdb=" N ASN G 236 " --> pdb=" O ASN G 251 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN G 251 " --> pdb=" O ASN G 236 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER G 238 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE G 249 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY G 240 " --> pdb=" O ARG G 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 289 through 292 removed outlier: 6.536A pdb=" N VAL G 590 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU G 608 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL G 592 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL G 564 " --> pdb=" O MET G 591 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL G 593 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL G 566 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE G 313 " --> pdb=" O VAL G 565 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU G 567 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE G 315 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N TYR G 338 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY G 314 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 445 through 448 removed outlier: 6.449A pdb=" N LEU G 429 " --> pdb=" O TRP G 445 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR G 447 " --> pdb=" O LEU G 429 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL G 431 " --> pdb=" O TYR G 447 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA G 374 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE G 499 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU G 376 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY G 501 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LEU G 378 " --> pdb=" O GLY G 501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 618 through 621 removed outlier: 3.725A pdb=" N VAL G 783 " --> pdb=" O ALA G 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 702 through 703 removed outlier: 6.704A pdb=" N LEU G 702 " --> pdb=" O THR G 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 899 through 900 removed outlier: 3.648A pdb=" N TRP G 810 " --> pdb=" O LEU G 900 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG G 811 " --> pdb=" O VAL G 882 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU G 884 " --> pdb=" O ARG G 811 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA G 813 " --> pdb=" O LEU G 884 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE G 840 " --> pdb=" O GLU G 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.834A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 65 through 66 removed outlier: 4.049A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AC6, first strand: chain 'L' and resid 60 through 70 removed outlier: 8.401A pdb=" N GLN L 62 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU L 81 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU L 64 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LEU L 79 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR L 66 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N PHE L 77 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 61 through 62 1901 hydrogen bonds defined for protein. 5475 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: 7.26 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 15233 1.43 - 1.65: 20397 1.65 - 1.86: 366 1.86 - 2.07: 0 2.07 - 2.29: 92 Bond restraints: 36088 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" CB CSX E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.371 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CB CSX B 102 " pdb=" SG CSX B 102 " ideal model delta sigma weight residual 1.831 1.761 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 46444 1.71 - 3.41: 2180 3.41 - 5.12: 409 5.12 - 6.82: 69 6.82 - 8.53: 13 Bond angle restraints: 49115 Sorted by residual: angle pdb=" N CYS B 64 " pdb=" CA CYS B 64 " pdb=" CB CYS B 64 " ideal model delta sigma weight residual 114.17 109.07 5.10 1.14e+00 7.69e-01 2.00e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.50 4.87 1.34e+00 5.57e-01 1.32e+01 angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA CYS G 228 " pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " ideal model delta sigma weight residual 114.40 122.67 -8.27 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N VAL N 221 " pdb=" CA VAL N 221 " pdb=" C VAL N 221 " ideal model delta sigma weight residual 108.88 115.92 -7.04 2.16e+00 2.14e-01 1.06e+01 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19143 17.93 - 35.86: 1613 35.86 - 53.78: 279 53.78 - 71.71: 51 71.71 - 89.64: 19 Dihedral angle restraints: 21105 sinusoidal: 7917 harmonic: 13188 Sorted by residual: dihedral pdb=" CA TRP L 535 " pdb=" C TRP L 535 " pdb=" N TYR L 536 " pdb=" CA TYR L 536 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL K 23 " pdb=" C VAL K 23 " pdb=" N ILE K 24 " pdb=" CA ILE K 24 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR L 237 " pdb=" C THR L 237 " pdb=" N TRP L 238 " pdb=" CA TRP L 238 " ideal model delta harmonic sigma weight residual 180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 21102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4329 0.053 - 0.105: 1028 0.105 - 0.158: 178 0.158 - 0.211: 16 0.211 - 0.264: 3 Chirality restraints: 5554 Sorted by residual: chirality pdb=" CA PHE L 341 " pdb=" N PHE L 341 " pdb=" C PHE L 341 " pdb=" CB PHE L 341 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL L 35 " pdb=" CA VAL L 35 " pdb=" CG1 VAL L 35 " pdb=" CG2 VAL L 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU L 299 " pdb=" CB LEU L 299 " pdb=" CD1 LEU L 299 " pdb=" CD2 LEU L 299 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5551 not shown) Planarity restraints: 6256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 356 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C PRO F 356 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO F 356 " 0.026 2.00e-02 2.50e+03 pdb=" N CYS F 357 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU G 457 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU G 457 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY G 458 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 30 " 0.031 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP M 30 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 30 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP M 30 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 30 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 30 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 30 " 0.004 2.00e-02 2.50e+03 ... (remaining 6253 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 143 2.51 - 3.11: 25717 3.11 - 3.71: 56073 3.71 - 4.30: 77405 4.30 - 4.90: 129902 Nonbonded interactions: 289240 Sorted by model distance: nonbonded pdb=" OG SER K 67 " pdb=" OH TYR A 84 " model vdw 1.913 3.040 nonbonded pdb=" OE1 GLN G 632 " pdb="CA CA G1005 " model vdw 2.179 2.510 nonbonded pdb=" OE2 GLU G 624 " pdb=" NH2 ARG G 784 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.218 3.120 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.222 3.040 ... (remaining 289235 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 group one per residue 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.160 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 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 : 0.005 0.256 36124 Z= 0.230 Angle : 1.382 71.878 49208 Z= 0.459 Chirality : 0.046 0.264 5554 Planarity : 0.006 0.082 6256 Dihedral : 13.860 89.640 12665 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.85 % Allowed : 2.78 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.68 (0.11), residues: 4573 helix: -0.92 (0.09), residues: 2476 sheet: -0.39 (0.30), residues: 299 loop : -1.33 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 597 TYR 0.054 0.002 TYR N 397 PHE 0.046 0.003 PHE N 396 TRP 0.062 0.002 TRP M 30 HIS 0.012 0.001 HIS F 400 Details of bonding type rmsd covalent geometry : bond 0.00513 (36088) covalent geometry : angle 0.85031 (49115) hydrogen bonds : bond 0.18090 ( 1899) hydrogen bonds : angle 6.77720 ( 5475) metal coordination : bond 0.05815 ( 36) metal coordination : angle 25.06212 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1465 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 TYR cc_start: 0.7037 (t80) cc_final: 0.6606 (t80) REVERT: B 103 PHE cc_start: 0.6145 (m-80) cc_final: 0.4870 (m-80) REVERT: B 106 MET cc_start: 0.6777 (ppp) cc_final: 0.6357 (ppp) REVERT: B 113 LEU cc_start: 0.8543 (mp) cc_final: 0.8221 (mt) REVERT: B 146 ASP cc_start: 0.7977 (p0) cc_final: 0.7652 (t0) REVERT: D 18 ASP cc_start: 0.7750 (p0) cc_final: 0.7481 (p0) REVERT: D 77 ASP cc_start: 0.7073 (t70) cc_final: 0.6677 (t70) REVERT: D 91 ASP cc_start: 0.6876 (m-30) cc_final: 0.5994 (t0) REVERT: D 110 LYS cc_start: 0.7900 (mttp) cc_final: 0.7569 (mtpp) REVERT: D 294 THR cc_start: 0.8191 (m) cc_final: 0.7821 (p) REVERT: D 496 THR cc_start: 0.8488 (m) cc_final: 0.8253 (m) REVERT: D 553 TYR cc_start: 0.7832 (t80) cc_final: 0.7630 (t80) REVERT: D 555 THR cc_start: 0.8417 (m) cc_final: 0.8214 (p) REVERT: E 45 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8189 (tptp) REVERT: E 142 ASN cc_start: 0.7445 (m-40) cc_final: 0.7226 (m-40) REVERT: F 33 ASN cc_start: 0.8331 (t0) cc_final: 0.7755 (t0) REVERT: F 186 LEU cc_start: 0.9293 (tt) cc_final: 0.9087 (tt) REVERT: G 21 GLU cc_start: 0.7914 (pt0) cc_final: 0.7563 (pt0) REVERT: G 55 ASN cc_start: 0.7397 (p0) cc_final: 0.7184 (p0) REVERT: G 78 SER cc_start: 0.8882 (t) cc_final: 0.8397 (p) REVERT: G 111 ASN cc_start: 0.7767 (t0) cc_final: 0.7278 (t0) REVERT: G 137 ASN cc_start: 0.8227 (m-40) cc_final: 0.7393 (m110) REVERT: G 147 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6637 (mm-30) REVERT: G 173 TYR cc_start: 0.8433 (m-80) cc_final: 0.7690 (m-80) REVERT: G 311 LYS cc_start: 0.7702 (tttt) cc_final: 0.7162 (tttp) REVERT: G 497 LEU cc_start: 0.8731 (tp) cc_final: 0.8492 (tp) REVERT: G 537 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7168 (t0) REVERT: G 539 MET cc_start: 0.6546 (mmt) cc_final: 0.6293 (mmm) REVERT: G 548 SER cc_start: 0.5870 (p) cc_final: 0.4883 (t) REVERT: G 589 LEU cc_start: 0.7814 (tp) cc_final: 0.7277 (mm) REVERT: G 653 HIS cc_start: 0.6335 (t-90) cc_final: 0.5699 (t-170) REVERT: G 663 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7468 (mm-30) REVERT: G 665 ASP cc_start: 0.6118 (t0) cc_final: 0.5755 (p0) REVERT: G 671 HIS cc_start: 0.6622 (m170) cc_final: 0.5967 (t-90) REVERT: G 772 VAL cc_start: 0.8491 (p) cc_final: 0.7585 (p) REVERT: G 804 GLN cc_start: 0.7280 (tp40) cc_final: 0.6888 (tm-30) REVERT: G 810 TRP cc_start: 0.7301 (m100) cc_final: 0.7058 (m100) REVERT: G 905 GLU cc_start: 0.4938 (mp0) cc_final: 0.3491 (mp0) REVERT: I 78 GLN cc_start: 0.8099 (tp40) cc_final: 0.7879 (tp40) REVERT: I 106 GLU cc_start: 0.7412 (tt0) cc_final: 0.7100 (tt0) REVERT: I 126 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7315 (tptp) REVERT: I 162 ASP cc_start: 0.5712 (t70) cc_final: 0.5119 (t70) REVERT: K 39 ILE cc_start: 0.5900 (mt) cc_final: 0.5079 (mt) REVERT: K 98 MET cc_start: 0.5827 (ptt) cc_final: 0.5354 (ppp) REVERT: J 1 MET cc_start: 0.2903 (tpt) cc_final: 0.2695 (tmm) REVERT: J 33 ILE cc_start: 0.6609 (mm) cc_final: 0.6324 (mm) REVERT: J 112 LEU cc_start: 0.6216 (pp) cc_final: 0.5851 (mt) REVERT: J 134 PHE cc_start: 0.6892 (t80) cc_final: 0.6630 (t80) REVERT: H 88 MET cc_start: 0.5745 (mpp) cc_final: 0.4599 (mtp) REVERT: H 237 PHE cc_start: 0.6026 (m-10) cc_final: 0.5420 (t80) REVERT: M 63 TRP cc_start: 0.3370 (m-90) cc_final: 0.2393 (m-10) REVERT: M 336 LEU cc_start: 0.8522 (tp) cc_final: 0.6591 (pt) REVERT: M 418 VAL cc_start: 0.6863 (p) cc_final: 0.6603 (m) REVERT: M 467 MET cc_start: 0.7724 (ptt) cc_final: 0.7260 (mtp) REVERT: M 486 LEU cc_start: 0.7241 (mt) cc_final: 0.6679 (mt) REVERT: L 158 TYR cc_start: 0.5226 (p90) cc_final: 0.4078 (p90) REVERT: L 159 THR cc_start: 0.8109 (p) cc_final: 0.7782 (p) REVERT: L 191 GLU cc_start: 0.6007 (tp30) cc_final: 0.5639 (tp30) REVERT: L 203 LEU cc_start: 0.8131 (tt) cc_final: 0.6523 (mp) REVERT: L 212 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6350 (p0) REVERT: L 216 MET cc_start: 0.2399 (mpp) cc_final: 0.1289 (mmt) REVERT: L 246 PRO cc_start: 0.4701 (Cg_exo) cc_final: 0.4499 (Cg_endo) REVERT: L 270 HIS cc_start: 0.7885 (p-80) cc_final: 0.7483 (p-80) REVERT: L 275 MET cc_start: 0.3948 (mmm) cc_final: 0.3699 (mmt) REVERT: L 347 LEU cc_start: -0.3654 (mt) cc_final: -0.4286 (pp) REVERT: L 574 VAL cc_start: 0.4241 (t) cc_final: 0.4021 (p) REVERT: L 592 ARG cc_start: 0.5481 (mtt90) cc_final: 0.4227 (ptt90) REVERT: N 8 LEU cc_start: 0.6462 (mt) cc_final: 0.5598 (pp) REVERT: N 61 MET cc_start: 0.3279 (ppp) cc_final: 0.2707 (ptt) REVERT: N 74 MET cc_start: 0.4448 (mtp) cc_final: 0.4199 (mmm) REVERT: N 203 LEU cc_start: 0.5885 (tp) cc_final: 0.5591 (mt) REVERT: N 379 MET cc_start: 0.5711 (mmt) cc_final: 0.5127 (mmt) REVERT: N 427 ARG cc_start: 0.6742 (mtm180) cc_final: 0.6438 (mmm160) outliers start: 30 outliers final: 8 residues processed: 1482 average time/residue: 0.2247 time to fit residues: 529.7832 Evaluate side-chains 1091 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1081 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain N residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 279 ASN D 340 GLN D 397 ASN D 517 GLN E 78 GLN E 100 ASN E 119 GLN E 150 HIS F 142 ASN F 304 HIS F 400 HIS ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 229 GLN G 605 HIS G 766 ASN I 128 GLN K 40 ASN M 335 GLN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS L 135 ASN L 232 GLN L 338 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.245767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.200646 restraints weight = 53272.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.205364 restraints weight = 63182.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.203922 restraints weight = 22816.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.204528 restraints weight = 24169.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.204295 restraints weight = 17630.608| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 36124 Z= 0.179 Angle : 1.058 65.266 49208 Z= 0.375 Chirality : 0.045 0.260 5554 Planarity : 0.006 0.071 6256 Dihedral : 5.261 83.189 5004 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.54 % Allowed : 13.83 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.72 (0.12), residues: 4573 helix: 0.07 (0.10), residues: 2545 sheet: -0.16 (0.31), residues: 283 loop : -1.22 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 172 TYR 0.034 0.002 TYR M 435 PHE 0.033 0.002 PHE M 15 TRP 0.029 0.002 TRP M 30 HIS 0.010 0.001 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00395 (36088) covalent geometry : angle 0.72579 (49115) hydrogen bonds : bond 0.05001 ( 1899) hydrogen bonds : angle 4.97707 ( 5475) metal coordination : bond 0.01698 ( 36) metal coordination : angle 17.71912 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1137 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7638 (t60) cc_final: 0.7203 (t60) REVERT: B 57 TYR cc_start: 0.6962 (t80) cc_final: 0.6473 (t80) REVERT: B 103 PHE cc_start: 0.6276 (m-80) cc_final: 0.5603 (m-80) REVERT: B 106 MET cc_start: 0.7240 (ppp) cc_final: 0.6678 (ppp) REVERT: B 109 VAL cc_start: 0.7996 (t) cc_final: 0.7745 (t) REVERT: B 113 LEU cc_start: 0.8739 (mp) cc_final: 0.8431 (mp) REVERT: B 146 ASP cc_start: 0.8133 (p0) cc_final: 0.7770 (t0) REVERT: D 51 GLU cc_start: 0.5682 (mm-30) cc_final: 0.4902 (mp0) REVERT: D 60 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (mp) REVERT: D 76 MET cc_start: 0.7754 (ttp) cc_final: 0.7461 (ttm) REVERT: D 77 ASP cc_start: 0.7232 (t70) cc_final: 0.6818 (t70) REVERT: D 91 ASP cc_start: 0.6781 (m-30) cc_final: 0.6345 (t0) REVERT: D 110 LYS cc_start: 0.7916 (mttp) cc_final: 0.7543 (mtpp) REVERT: D 195 PHE cc_start: 0.6088 (p90) cc_final: 0.5465 (t80) REVERT: D 259 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7660 (mm110) REVERT: D 392 LYS cc_start: 0.7574 (pttm) cc_final: 0.7159 (mmtm) REVERT: D 444 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: D 447 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6216 (p0) REVERT: D 449 GLU cc_start: 0.5637 (pp20) cc_final: 0.5318 (pp20) REVERT: D 524 MET cc_start: 0.8334 (mmm) cc_final: 0.7962 (mmm) REVERT: D 541 SER cc_start: 0.6557 (p) cc_final: 0.6341 (t) REVERT: D 542 TYR cc_start: 0.6509 (m-80) cc_final: 0.6004 (m-80) REVERT: D 553 TYR cc_start: 0.7988 (t80) cc_final: 0.7585 (t80) REVERT: D 555 THR cc_start: 0.8635 (m) cc_final: 0.8341 (p) REVERT: E 18 GLU cc_start: 0.7975 (mp0) cc_final: 0.7248 (pm20) REVERT: E 25 GLU cc_start: 0.6963 (tp30) cc_final: 0.6706 (tp30) REVERT: E 45 LYS cc_start: 0.8506 (tmmt) cc_final: 0.8012 (tptt) REVERT: E 90 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6449 (mtm-85) REVERT: E 106 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6937 (tm-30) REVERT: E 148 ASP cc_start: 0.7357 (t0) cc_final: 0.7088 (t0) REVERT: F 9 GLU cc_start: 0.7115 (tp30) cc_final: 0.6620 (tp30) REVERT: F 39 ARG cc_start: 0.4825 (OUTLIER) cc_final: 0.4462 (tmm160) REVERT: F 40 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.6006 (ptpp) REVERT: F 50 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8850 (mm) REVERT: F 94 MET cc_start: 0.6801 (tpp) cc_final: 0.6387 (ttm) REVERT: F 101 ASP cc_start: 0.7779 (m-30) cc_final: 0.6862 (m-30) REVERT: F 219 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.6939 (m) REVERT: G 21 GLU cc_start: 0.8331 (pt0) cc_final: 0.7887 (pt0) REVERT: G 55 ASN cc_start: 0.7680 (p0) cc_final: 0.7381 (p0) REVERT: G 78 SER cc_start: 0.8865 (t) cc_final: 0.8393 (p) REVERT: G 137 ASN cc_start: 0.8299 (m-40) cc_final: 0.7592 (m110) REVERT: G 147 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6725 (mm-30) REVERT: G 173 TYR cc_start: 0.8721 (m-80) cc_final: 0.8017 (m-80) REVERT: G 395 GLN cc_start: 0.7642 (mm-40) cc_final: 0.6823 (mm-40) REVERT: G 497 LEU cc_start: 0.8618 (tp) cc_final: 0.8307 (tp) REVERT: G 537 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7470 (t0) REVERT: G 539 MET cc_start: 0.6382 (mmt) cc_final: 0.5999 (mmm) REVERT: G 589 LEU cc_start: 0.7788 (tp) cc_final: 0.7373 (mm) REVERT: G 590 VAL cc_start: 0.8087 (m) cc_final: 0.7868 (m) REVERT: G 653 HIS cc_start: 0.6891 (t-90) cc_final: 0.6689 (t-170) REVERT: G 671 HIS cc_start: 0.6804 (m170) cc_final: 0.6293 (t-90) REVERT: G 755 TRP cc_start: 0.8591 (t60) cc_final: 0.8297 (t60) REVERT: G 760 ASN cc_start: 0.8055 (m-40) cc_final: 0.7847 (m-40) REVERT: G 825 SER cc_start: 0.8892 (p) cc_final: 0.8503 (m) REVERT: I 47 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6809 (ttm110) REVERT: I 81 GLU cc_start: 0.8299 (tt0) cc_final: 0.8060 (tt0) REVERT: I 106 GLU cc_start: 0.7443 (tt0) cc_final: 0.7097 (tt0) REVERT: I 136 ASP cc_start: 0.8658 (m-30) cc_final: 0.8268 (m-30) REVERT: K 31 MET cc_start: 0.6147 (mpp) cc_final: 0.5671 (mpp) REVERT: J 1 MET cc_start: 0.3163 (tpt) cc_final: 0.2320 (tmm) REVERT: J 5 PHE cc_start: 0.3330 (t80) cc_final: 0.1941 (m-80) REVERT: J 112 LEU cc_start: 0.6325 (pp) cc_final: 0.5984 (mt) REVERT: J 134 PHE cc_start: 0.6680 (t80) cc_final: 0.6322 (t80) REVERT: A 107 ILE cc_start: 0.8075 (pt) cc_final: 0.7791 (pt) REVERT: H 88 MET cc_start: 0.5583 (mpp) cc_final: 0.4027 (mmt) REVERT: H 311 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5838 (mp) REVERT: M 67 PHE cc_start: 0.1540 (t80) cc_final: 0.1076 (t80) REVERT: M 75 PHE cc_start: 0.6064 (m-80) cc_final: 0.5638 (m-80) REVERT: M 151 TYR cc_start: 0.2656 (t80) cc_final: 0.2003 (t80) REVERT: M 336 LEU cc_start: 0.7698 (tp) cc_final: 0.5872 (tp) REVERT: M 356 PHE cc_start: 0.4445 (m-10) cc_final: 0.4200 (m-10) REVERT: M 427 PHE cc_start: 0.5556 (m-80) cc_final: 0.5343 (m-80) REVERT: M 463 ARG cc_start: 0.5973 (ppt170) cc_final: 0.5617 (tmm160) REVERT: L 107 MET cc_start: 0.6485 (ptt) cc_final: 0.5481 (ptt) REVERT: L 137 LEU cc_start: 0.0621 (OUTLIER) cc_final: 0.0274 (mp) REVERT: L 191 GLU cc_start: 0.6306 (tp30) cc_final: 0.5839 (tp30) REVERT: L 195 LEU cc_start: -0.0720 (OUTLIER) cc_final: -0.2508 (mp) REVERT: L 214 MET cc_start: 0.3500 (tmm) cc_final: 0.3281 (tmm) REVERT: L 270 HIS cc_start: 0.8279 (p-80) cc_final: 0.8045 (p90) REVERT: L 319 MET cc_start: 0.4764 (mmm) cc_final: 0.4498 (mmm) REVERT: L 592 ARG cc_start: 0.4691 (mtt90) cc_final: 0.3497 (ttp-110) REVERT: L 594 TYR cc_start: 0.5364 (m-10) cc_final: 0.4906 (m-10) REVERT: N 8 LEU cc_start: 0.6722 (mt) cc_final: 0.6285 (tp) REVERT: N 74 MET cc_start: 0.5484 (mtp) cc_final: 0.5142 (ptt) REVERT: N 241 PHE cc_start: 0.7264 (t80) cc_final: 0.7040 (t80) REVERT: N 286 LEU cc_start: 0.8157 (mp) cc_final: 0.7883 (mp) REVERT: N 379 MET cc_start: 0.6045 (mmt) cc_final: 0.5235 (mmt) REVERT: N 427 ARG cc_start: 0.6830 (mtm180) cc_final: 0.6348 (mmm160) outliers start: 125 outliers final: 71 residues processed: 1195 average time/residue: 0.2182 time to fit residues: 420.1739 Evaluate side-chains 1129 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1047 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 472 VAL Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 353 optimal weight: 6.9990 chunk 152 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 205 optimal weight: 0.9990 chunk 344 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 397 ASN D 472 GLN E 78 GLN E 119 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 763 GLN G 899 HIS I 78 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS N 180 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.242939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.197098 restraints weight = 54294.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.201079 restraints weight = 72509.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199160 restraints weight = 32119.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.199438 restraints weight = 25108.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.199826 restraints weight = 18448.696| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 36124 Z= 0.192 Angle : 1.020 57.511 49208 Z= 0.364 Chirality : 0.046 0.312 5554 Planarity : 0.005 0.067 6256 Dihedral : 5.147 84.025 4997 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.34 % Allowed : 17.04 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.33 (0.12), residues: 4573 helix: 0.42 (0.10), residues: 2552 sheet: -0.07 (0.31), residues: 284 loop : -1.12 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 369 TYR 0.031 0.002 TYR L 189 PHE 0.044 0.002 PHE H 278 TRP 0.029 0.002 TRP H 260 HIS 0.010 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00433 (36088) covalent geometry : angle 0.70723 (49115) hydrogen bonds : bond 0.04568 ( 1899) hydrogen bonds : angle 4.81176 ( 5475) metal coordination : bond 0.01752 ( 36) metal coordination : angle 16.91167 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1118 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7579 (t60) cc_final: 0.7242 (t60) REVERT: B 57 TYR cc_start: 0.6997 (t80) cc_final: 0.6570 (t80) REVERT: B 103 PHE cc_start: 0.6299 (m-80) cc_final: 0.5445 (m-80) REVERT: B 106 MET cc_start: 0.7427 (ppp) cc_final: 0.7104 (ppp) REVERT: B 109 VAL cc_start: 0.7988 (t) cc_final: 0.7753 (t) REVERT: B 112 ARG cc_start: 0.7110 (mmp80) cc_final: 0.6665 (mmt180) REVERT: B 113 LEU cc_start: 0.8772 (mp) cc_final: 0.8471 (mt) REVERT: D 48 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7197 (pt) REVERT: D 91 ASP cc_start: 0.6900 (m-30) cc_final: 0.6113 (t0) REVERT: D 150 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.6321 (p0) REVERT: D 347 GLU cc_start: 0.7658 (pt0) cc_final: 0.7108 (pt0) REVERT: D 444 GLU cc_start: 0.7169 (pt0) cc_final: 0.6945 (pt0) REVERT: D 447 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.6101 (p0) REVERT: D 524 MET cc_start: 0.8217 (mmm) cc_final: 0.7938 (mmm) REVERT: D 553 TYR cc_start: 0.8151 (t80) cc_final: 0.7519 (t80) REVERT: E 18 GLU cc_start: 0.8370 (mp0) cc_final: 0.7956 (pm20) REVERT: E 45 LYS cc_start: 0.8599 (tmmt) cc_final: 0.8045 (tptt) REVERT: E 106 GLN cc_start: 0.7235 (tm-30) cc_final: 0.7003 (tm-30) REVERT: E 125 ARG cc_start: 0.6434 (tpp80) cc_final: 0.5754 (tpp80) REVERT: E 129 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7634 (mm) REVERT: E 148 ASP cc_start: 0.7104 (t0) cc_final: 0.6820 (t0) REVERT: F 252 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: G 78 SER cc_start: 0.8946 (t) cc_final: 0.8469 (p) REVERT: G 221 MET cc_start: 0.8615 (mmt) cc_final: 0.7820 (mmm) REVERT: G 311 LYS cc_start: 0.7559 (tttt) cc_final: 0.7322 (tttt) REVERT: G 367 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6551 (ttt180) REVERT: G 395 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6398 (mm-40) REVERT: G 497 LEU cc_start: 0.8585 (tp) cc_final: 0.8283 (tp) REVERT: G 537 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7611 (t0) REVERT: G 572 HIS cc_start: 0.7392 (m-70) cc_final: 0.6960 (m170) REVERT: G 589 LEU cc_start: 0.7841 (tp) cc_final: 0.7437 (mm) REVERT: G 597 ARG cc_start: 0.7445 (ttm170) cc_final: 0.6900 (ttm-80) REVERT: G 671 HIS cc_start: 0.6888 (m170) cc_final: 0.6301 (t-90) REVERT: G 676 VAL cc_start: 0.8589 (p) cc_final: 0.8373 (m) REVERT: G 726 GLN cc_start: 0.6957 (mt0) cc_final: 0.6381 (mt0) REVERT: G 760 ASN cc_start: 0.8260 (m-40) cc_final: 0.8026 (m-40) REVERT: I 81 GLU cc_start: 0.8493 (tt0) cc_final: 0.8198 (tt0) REVERT: I 106 GLU cc_start: 0.7419 (tt0) cc_final: 0.7069 (tt0) REVERT: I 148 TYR cc_start: 0.8303 (t80) cc_final: 0.8051 (t80) REVERT: K 36 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6165 (mm-30) REVERT: J 1 MET cc_start: 0.3202 (tpt) cc_final: 0.2395 (tmm) REVERT: J 5 PHE cc_start: 0.3486 (t80) cc_final: 0.1899 (m-80) REVERT: J 112 LEU cc_start: 0.6357 (pp) cc_final: 0.5991 (mt) REVERT: H 88 MET cc_start: 0.5561 (mpp) cc_final: 0.4116 (mmt) REVERT: H 143 LEU cc_start: 0.4025 (OUTLIER) cc_final: 0.3788 (tp) REVERT: H 311 ILE cc_start: 0.6036 (OUTLIER) cc_final: 0.5558 (mp) REVERT: M 118 LEU cc_start: 0.1850 (pp) cc_final: 0.0527 (tt) REVERT: M 156 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.5957 (tp) REVERT: M 276 LEU cc_start: 0.7532 (tp) cc_final: 0.7210 (mt) REVERT: M 374 MET cc_start: 0.5806 (pmm) cc_final: 0.5452 (pmm) REVERT: M 460 MET cc_start: -0.0228 (OUTLIER) cc_final: -0.2081 (ppp) REVERT: M 475 LEU cc_start: 0.7642 (pp) cc_final: 0.6063 (tp) REVERT: L 27 GLU cc_start: 0.6209 (pm20) cc_final: 0.5285 (pm20) REVERT: L 113 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.4258 (t80) REVERT: L 137 LEU cc_start: 0.0701 (OUTLIER) cc_final: 0.0474 (mp) REVERT: L 151 TYR cc_start: 0.4861 (t80) cc_final: 0.4603 (t80) REVERT: L 168 MET cc_start: -0.1619 (ptt) cc_final: -0.1993 (ptt) REVERT: L 191 GLU cc_start: 0.6459 (tp30) cc_final: 0.6054 (tp30) REVERT: L 195 LEU cc_start: -0.1162 (OUTLIER) cc_final: -0.2922 (tt) REVERT: L 214 MET cc_start: 0.3652 (tmm) cc_final: 0.3396 (tmm) REVERT: L 239 LEU cc_start: 0.5992 (mp) cc_final: 0.5225 (mm) REVERT: L 313 MET cc_start: 0.4537 (mtp) cc_final: 0.4316 (mtp) REVERT: L 568 MET cc_start: 0.6393 (ptm) cc_final: 0.5574 (ptt) REVERT: L 592 ARG cc_start: 0.4937 (mtt90) cc_final: 0.3606 (ttp80) REVERT: N 8 LEU cc_start: 0.6913 (mt) cc_final: 0.6711 (mp) REVERT: N 68 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.5911 (tpt-90) REVERT: N 74 MET cc_start: 0.5754 (mtp) cc_final: 0.5540 (mmm) REVERT: N 140 PHE cc_start: 0.4710 (m-80) cc_final: 0.4292 (m-80) REVERT: N 203 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6275 (tp) REVERT: N 286 LEU cc_start: 0.8115 (mp) cc_final: 0.7814 (mp) REVERT: N 309 LEU cc_start: 0.7327 (mt) cc_final: 0.6556 (mt) REVERT: N 329 TYR cc_start: 0.3606 (t80) cc_final: 0.3404 (t80) REVERT: N 379 MET cc_start: 0.6090 (mmt) cc_final: 0.5126 (mmt) REVERT: N 427 ARG cc_start: 0.7146 (mtm180) cc_final: 0.6761 (mmm160) outliers start: 153 outliers final: 103 residues processed: 1175 average time/residue: 0.2115 time to fit residues: 402.5478 Evaluate side-chains 1154 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1035 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 621 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 869 LEU Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 152 PHE Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 434 optimal weight: 0.8980 chunk 353 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 294 optimal weight: 9.9990 chunk 441 optimal weight: 0.8980 chunk 230 optimal weight: 0.0670 chunk 309 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 360 optimal weight: 40.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 78 GLN E 100 ASN E 119 GLN F 90 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 865 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN L 100 HIS L 270 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.244548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.199925 restraints weight = 54205.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.203911 restraints weight = 67556.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.202229 restraints weight = 25077.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.202677 restraints weight = 27048.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.202420 restraints weight = 18905.122| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36124 Z= 0.147 Angle : 0.910 46.444 49208 Z= 0.345 Chirality : 0.044 0.357 5554 Planarity : 0.005 0.063 6256 Dihedral : 4.999 86.048 4995 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.17 % Allowed : 20.01 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4573 helix: 0.65 (0.10), residues: 2533 sheet: -0.06 (0.29), residues: 300 loop : -1.06 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 172 TYR 0.045 0.002 TYR L 189 PHE 0.044 0.002 PHE H 278 TRP 0.030 0.001 TRP F 262 HIS 0.017 0.001 HIS L 270 Details of bonding type rmsd covalent geometry : bond 0.00328 (36088) covalent geometry : angle 0.67757 (49115) hydrogen bonds : bond 0.04151 ( 1899) hydrogen bonds : angle 4.69251 ( 5475) metal coordination : bond 0.01299 ( 36) metal coordination : angle 13.99638 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1073 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7610 (t60) cc_final: 0.7202 (t60) REVERT: B 103 PHE cc_start: 0.6232 (m-80) cc_final: 0.5639 (m-80) REVERT: B 106 MET cc_start: 0.7351 (ppp) cc_final: 0.6616 (ppp) REVERT: B 109 VAL cc_start: 0.7977 (t) cc_final: 0.7733 (t) REVERT: B 112 ARG cc_start: 0.7105 (mmp80) cc_final: 0.6676 (mmt180) REVERT: B 204 LYS cc_start: 0.7556 (ptpp) cc_final: 0.7128 (ptpp) REVERT: D 48 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7371 (pt) REVERT: D 60 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8215 (mp) REVERT: D 91 ASP cc_start: 0.7029 (m-30) cc_final: 0.6506 (m-30) REVERT: D 150 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6684 (p0) REVERT: D 305 MET cc_start: 0.8064 (ttp) cc_final: 0.7777 (ttp) REVERT: D 447 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5982 (p0) REVERT: D 553 TYR cc_start: 0.8048 (t80) cc_final: 0.7460 (t80) REVERT: E 18 GLU cc_start: 0.8555 (mp0) cc_final: 0.8018 (pm20) REVERT: E 19 ARG cc_start: 0.6679 (tpt170) cc_final: 0.6295 (tpt90) REVERT: E 45 LYS cc_start: 0.8069 (tmmt) cc_final: 0.7832 (tptt) REVERT: E 144 MET cc_start: 0.7501 (ptm) cc_final: 0.7173 (ptm) REVERT: F 1 MET cc_start: 0.6521 (ppp) cc_final: 0.2412 (tpp) REVERT: F 30 ARG cc_start: 0.6028 (tpm170) cc_final: 0.5441 (tpm170) REVERT: F 252 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: G 26 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7061 (mp) REVERT: G 78 SER cc_start: 0.8828 (t) cc_final: 0.8302 (p) REVERT: G 221 MET cc_start: 0.8284 (mmt) cc_final: 0.7933 (mmt) REVERT: G 267 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8256 (mtp85) REVERT: G 311 LYS cc_start: 0.7565 (tttt) cc_final: 0.7315 (tttp) REVERT: G 367 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6533 (ttt180) REVERT: G 497 LEU cc_start: 0.8575 (tp) cc_final: 0.8268 (tp) REVERT: G 537 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7548 (t0) REVERT: G 539 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6092 (mmm) REVERT: G 572 HIS cc_start: 0.7423 (m-70) cc_final: 0.7005 (m170) REVERT: G 589 LEU cc_start: 0.7669 (tp) cc_final: 0.7323 (mm) REVERT: G 597 ARG cc_start: 0.7331 (ttm170) cc_final: 0.6864 (ttm-80) REVERT: G 667 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7482 (m) REVERT: G 784 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7733 (mtp85) REVERT: G 832 GLN cc_start: 0.6301 (mm-40) cc_final: 0.6021 (mm-40) REVERT: I 106 GLU cc_start: 0.7293 (tt0) cc_final: 0.7003 (tt0) REVERT: K 36 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6194 (mm-30) REVERT: J 112 LEU cc_start: 0.6370 (pp) cc_final: 0.6028 (mt) REVERT: A 73 MET cc_start: 0.6261 (tmm) cc_final: 0.5671 (ttt) REVERT: H 82 ILE cc_start: 0.7209 (tt) cc_final: 0.6002 (tt) REVERT: H 88 MET cc_start: 0.5311 (mpp) cc_final: 0.4329 (mmt) REVERT: H 237 PHE cc_start: 0.5443 (m-80) cc_final: 0.4488 (m-10) REVERT: H 311 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6056 (mp) REVERT: M 75 PHE cc_start: 0.6129 (m-80) cc_final: 0.5924 (m-80) REVERT: M 112 TYR cc_start: 0.3222 (p90) cc_final: 0.2967 (p90) REVERT: M 118 LEU cc_start: 0.3262 (pp) cc_final: 0.2523 (tt) REVERT: M 156 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.5786 (tp) REVERT: M 462 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5097 (mp) REVERT: M 475 LEU cc_start: 0.7644 (pp) cc_final: 0.6070 (tp) REVERT: L 115 ARG cc_start: 0.6008 (mtm-85) cc_final: 0.5533 (mtm-85) REVERT: L 117 PHE cc_start: 0.1083 (OUTLIER) cc_final: -0.0215 (m-80) REVERT: L 137 LEU cc_start: 0.0708 (OUTLIER) cc_final: 0.0431 (mp) REVERT: L 168 MET cc_start: -0.1826 (ptt) cc_final: -0.2028 (ptt) REVERT: L 191 GLU cc_start: 0.6366 (tp30) cc_final: 0.5921 (tp30) REVERT: L 239 LEU cc_start: 0.5492 (mp) cc_final: 0.4958 (mm) REVERT: L 243 MET cc_start: 0.3469 (mmt) cc_final: 0.3144 (mmt) REVERT: L 275 MET cc_start: 0.1514 (mmt) cc_final: 0.0236 (mmt) REVERT: L 313 MET cc_start: 0.4449 (mtp) cc_final: 0.4228 (mtp) REVERT: L 319 MET cc_start: 0.4991 (mmm) cc_final: 0.4694 (mmm) REVERT: L 565 LEU cc_start: 0.3082 (pt) cc_final: 0.2684 (tp) REVERT: L 592 ARG cc_start: 0.5152 (mtt90) cc_final: 0.3946 (ptt90) REVERT: L 598 MET cc_start: 0.6982 (mmp) cc_final: 0.5568 (mmp) REVERT: N 8 LEU cc_start: 0.6655 (mt) cc_final: 0.6114 (tp) REVERT: N 19 LEU cc_start: 0.5169 (tp) cc_final: 0.4814 (tp) REVERT: N 74 MET cc_start: 0.5678 (mtp) cc_final: 0.5447 (mmm) REVERT: N 140 PHE cc_start: 0.4679 (m-80) cc_final: 0.4255 (m-80) REVERT: N 286 LEU cc_start: 0.8188 (mp) cc_final: 0.7793 (mp) REVERT: N 297 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8264 (tt) REVERT: N 379 MET cc_start: 0.6090 (mmt) cc_final: 0.5120 (mmt) REVERT: N 427 ARG cc_start: 0.7060 (mtm180) cc_final: 0.6758 (mmm160) outliers start: 147 outliers final: 93 residues processed: 1133 average time/residue: 0.2163 time to fit residues: 397.8582 Evaluate side-chains 1138 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1029 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 840 ILE Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 117 PHE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 340 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 367 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 271 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 213 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN F 52 ASN F 258 ASN G 5 HIS G 196 ASN G 216 ASN G 236 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN M 49 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN L 100 HIS L 270 HIS N 57 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.232905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.186790 restraints weight = 53588.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.190643 restraints weight = 71095.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188124 restraints weight = 26591.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.188570 restraints weight = 30085.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.188195 restraints weight = 21086.629| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.220 36124 Z= 0.437 Angle : 1.486 73.169 49208 Z= 0.505 Chirality : 0.061 0.683 5554 Planarity : 0.008 0.112 6256 Dihedral : 6.087 84.384 4995 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.35 % Allowed : 20.86 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.03 (0.12), residues: 4573 helix: 0.02 (0.10), residues: 2546 sheet: -1.05 (0.29), residues: 294 loop : -1.57 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 125 TYR 0.040 0.003 TYR G 372 PHE 0.046 0.004 PHE H 278 TRP 0.036 0.003 TRP E 49 HIS 0.017 0.003 HIS L 334 Details of bonding type rmsd covalent geometry : bond 0.00975 (36088) covalent geometry : angle 0.95286 (49115) hydrogen bonds : bond 0.05846 ( 1899) hydrogen bonds : angle 5.49137 ( 5475) metal coordination : bond 0.03395 ( 36) metal coordination : angle 26.24333 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1051 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7637 (t60) cc_final: 0.7238 (t60) REVERT: B 109 VAL cc_start: 0.8016 (t) cc_final: 0.7802 (t) REVERT: B 112 ARG cc_start: 0.7410 (mmp80) cc_final: 0.7149 (mmt180) REVERT: B 113 LEU cc_start: 0.8937 (mp) cc_final: 0.8523 (mt) REVERT: D 16 HIS cc_start: 0.6470 (m-70) cc_final: 0.6073 (m-70) REVERT: D 60 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8318 (mp) REVERT: D 87 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6258 (mp) REVERT: D 264 TYR cc_start: 0.8848 (t80) cc_final: 0.8496 (t80) REVERT: D 382 TRP cc_start: 0.4969 (t60) cc_final: 0.3940 (t60) REVERT: D 386 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6105 (tmm-80) REVERT: D 390 TYR cc_start: 0.4769 (m-80) cc_final: 0.3990 (m-80) REVERT: D 392 LYS cc_start: 0.8172 (pttm) cc_final: 0.7458 (mmtm) REVERT: D 447 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6671 (p0) REVERT: D 460 TYR cc_start: 0.7144 (t80) cc_final: 0.6943 (t80) REVERT: D 484 MET cc_start: 0.7220 (tpp) cc_final: 0.7016 (ttm) REVERT: D 497 THR cc_start: 0.9599 (m) cc_final: 0.8996 (p) REVERT: D 553 TYR cc_start: 0.8155 (t80) cc_final: 0.7403 (t80) REVERT: E 18 GLU cc_start: 0.8537 (mp0) cc_final: 0.8126 (pm20) REVERT: E 100 ASN cc_start: 0.6541 (OUTLIER) cc_final: 0.6328 (t0) REVERT: E 103 GLN cc_start: 0.7165 (mp10) cc_final: 0.6874 (mp10) REVERT: E 139 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7376 (mtmm) REVERT: E 144 MET cc_start: 0.7404 (ptm) cc_final: 0.6631 (ptm) REVERT: E 162 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7708 (mt) REVERT: F 1 MET cc_start: 0.7094 (ppp) cc_final: 0.2501 (tpp) REVERT: F 9 GLU cc_start: 0.6846 (tp30) cc_final: 0.6624 (tp30) REVERT: F 30 ARG cc_start: 0.6115 (tpm170) cc_final: 0.5794 (tpm170) REVERT: F 135 GLU cc_start: 0.4883 (OUTLIER) cc_final: 0.4508 (tp30) REVERT: F 252 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: F 380 ASP cc_start: 0.8709 (m-30) cc_final: 0.8487 (m-30) REVERT: G 293 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8179 (mt) REVERT: G 354 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7482 (ttpt) REVERT: G 367 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6640 (ttt180) REVERT: G 537 ASN cc_start: 0.8422 (t0) cc_final: 0.7895 (t0) REVERT: G 572 HIS cc_start: 0.7979 (m-70) cc_final: 0.7493 (m170) REVERT: G 579 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6806 (mmp80) REVERT: G 621 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8395 (mt) REVERT: G 771 GLU cc_start: 0.6825 (tt0) cc_final: 0.6585 (tt0) REVERT: G 804 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.7000 (pp30) REVERT: G 862 TYR cc_start: 0.5505 (t80) cc_final: 0.5213 (t80) REVERT: K 53 TRP cc_start: 0.7184 (m100) cc_final: 0.6862 (m100) REVERT: J 64 MET cc_start: 0.7571 (mmp) cc_final: 0.7362 (mmm) REVERT: J 112 LEU cc_start: 0.6561 (pp) cc_final: 0.6341 (tp) REVERT: J 134 PHE cc_start: 0.7131 (t80) cc_final: 0.6904 (t80) REVERT: H 112 LEU cc_start: 0.2341 (OUTLIER) cc_final: 0.1822 (mm) REVERT: H 187 TRP cc_start: 0.4441 (m100) cc_final: 0.4231 (m100) REVERT: H 275 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (m) REVERT: H 310 LEU cc_start: 0.6423 (mt) cc_final: 0.6052 (mt) REVERT: H 311 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5503 (mp) REVERT: M 75 PHE cc_start: 0.6603 (m-80) cc_final: 0.6319 (m-80) REVERT: M 151 TYR cc_start: 0.2445 (t80) cc_final: 0.1901 (t80) REVERT: M 156 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5301 (tp) REVERT: M 460 MET cc_start: -0.0453 (OUTLIER) cc_final: -0.1383 (ptt) REVERT: M 462 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5003 (tt) REVERT: M 475 LEU cc_start: 0.7561 (pp) cc_final: 0.6131 (tp) REVERT: L 73 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.4486 (m-80) REVERT: L 113 TYR cc_start: 0.5829 (p90) cc_final: 0.5560 (p90) REVERT: L 117 PHE cc_start: 0.0943 (OUTLIER) cc_final: -0.0015 (m-80) REVERT: L 191 GLU cc_start: 0.6339 (tp30) cc_final: 0.5955 (tp30) REVERT: L 275 MET cc_start: 0.2130 (mmt) cc_final: 0.1200 (mmt) REVERT: L 305 LYS cc_start: 0.5575 (mmtt) cc_final: 0.5179 (mmtt) REVERT: L 306 ARG cc_start: 0.8123 (ptt90) cc_final: 0.4904 (mpp-170) REVERT: L 313 MET cc_start: 0.4404 (mtp) cc_final: 0.4194 (mtp) REVERT: L 565 LEU cc_start: 0.2613 (pt) cc_final: 0.2117 (tt) REVERT: L 592 ARG cc_start: 0.4846 (mtt90) cc_final: 0.3554 (ptt90) REVERT: L 598 MET cc_start: 0.7061 (mmp) cc_final: 0.5408 (mmp) REVERT: N 68 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6036 (tpt-90) REVERT: N 74 MET cc_start: 0.5863 (mtp) cc_final: 0.5635 (mtm) REVERT: N 140 PHE cc_start: 0.6018 (m-80) cc_final: 0.5227 (m-10) REVERT: N 151 ARG cc_start: 0.5820 (ptp-170) cc_final: 0.5069 (ttp-110) REVERT: N 286 LEU cc_start: 0.8151 (mp) cc_final: 0.7692 (mp) REVERT: N 289 LEU cc_start: 0.5366 (mp) cc_final: 0.4770 (tt) REVERT: N 379 MET cc_start: 0.6113 (mmt) cc_final: 0.5098 (mmt) REVERT: N 427 ARG cc_start: 0.7072 (mtm180) cc_final: 0.6676 (mmm160) outliers start: 224 outliers final: 145 residues processed: 1156 average time/residue: 0.2059 time to fit residues: 389.3781 Evaluate side-chains 1159 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 993 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 440 TYR Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 621 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 702 LEU Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 776 LEU Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 804 GLN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain G residue 903 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 15 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 117 PHE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 175 optimal weight: 0.6980 chunk 419 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 268 optimal weight: 7.9990 chunk 384 optimal weight: 20.0000 chunk 388 optimal weight: 50.0000 chunk 191 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN D 150 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN G 216 ASN ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 348 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.240117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.193696 restraints weight = 52957.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197870 restraints weight = 66650.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.196062 restraints weight = 28984.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.196287 restraints weight = 22991.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.196700 restraints weight = 16943.308| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36124 Z= 0.156 Angle : 1.073 69.385 49208 Z= 0.370 Chirality : 0.045 0.406 5554 Planarity : 0.005 0.067 6256 Dihedral : 5.296 88.193 4990 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.11 % Allowed : 24.26 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4573 helix: 0.51 (0.10), residues: 2520 sheet: -0.84 (0.30), residues: 288 loop : -1.36 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 87 TYR 0.043 0.002 TYR L 189 PHE 0.061 0.002 PHE L 320 TRP 0.022 0.001 TRP M 106 HIS 0.026 0.001 HIS L 270 Details of bonding type rmsd covalent geometry : bond 0.00350 (36088) covalent geometry : angle 0.71978 (49115) hydrogen bonds : bond 0.04335 ( 1899) hydrogen bonds : angle 4.88142 ( 5475) metal coordination : bond 0.01092 ( 36) metal coordination : angle 18.32636 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1041 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7244 (mmp80) cc_final: 0.6841 (mmt180) REVERT: B 170 MET cc_start: 0.8087 (ttp) cc_final: 0.7811 (ttp) REVERT: B 204 LYS cc_start: 0.7965 (ptpp) cc_final: 0.7616 (ptpp) REVERT: D 16 HIS cc_start: 0.6174 (m-70) cc_final: 0.5933 (m-70) REVERT: D 497 THR cc_start: 0.9495 (m) cc_final: 0.9208 (p) REVERT: D 532 MET cc_start: 0.7271 (pmm) cc_final: 0.6968 (pmm) REVERT: D 553 TYR cc_start: 0.8156 (t80) cc_final: 0.7523 (t80) REVERT: E 18 GLU cc_start: 0.8485 (mp0) cc_final: 0.8069 (pm20) REVERT: E 25 GLU cc_start: 0.6083 (tp30) cc_final: 0.5851 (tp30) REVERT: E 60 ASP cc_start: 0.7612 (t0) cc_final: 0.7183 (p0) REVERT: E 103 GLN cc_start: 0.6553 (mp10) cc_final: 0.6159 (mp10) REVERT: E 144 MET cc_start: 0.7128 (ptm) cc_final: 0.6364 (ptm) REVERT: F 1 MET cc_start: 0.7243 (ppp) cc_final: 0.2853 (tpp) REVERT: F 158 LYS cc_start: 0.7325 (tptt) cc_final: 0.7052 (tppt) REVERT: F 165 PHE cc_start: 0.7417 (t80) cc_final: 0.7155 (t80) REVERT: F 252 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: F 262 TRP cc_start: 0.7832 (m-90) cc_final: 0.7386 (m-90) REVERT: F 358 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7735 (ttp80) REVERT: G 55 ASN cc_start: 0.7596 (p0) cc_final: 0.7333 (p0) REVERT: G 136 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7388 (mmt-90) REVERT: G 159 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7937 (ttp-170) REVERT: G 221 MET cc_start: 0.8551 (mmt) cc_final: 0.8071 (mmm) REVERT: G 293 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7595 (mt) REVERT: G 354 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7378 (ttpt) REVERT: G 361 ILE cc_start: 0.7411 (mm) cc_final: 0.7124 (mt) REVERT: G 367 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6606 (ttt180) REVERT: G 537 ASN cc_start: 0.8301 (t0) cc_final: 0.7510 (t0) REVERT: G 549 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8110 (mt) REVERT: G 572 HIS cc_start: 0.7672 (m-70) cc_final: 0.7061 (m170) REVERT: G 597 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6738 (ttm-80) REVERT: G 601 MET cc_start: 0.7635 (mtt) cc_final: 0.7366 (mtt) REVERT: G 651 TRP cc_start: 0.7627 (m100) cc_final: 0.7074 (m100) REVERT: G 886 MET cc_start: 0.7312 (mmp) cc_final: 0.7083 (mmm) REVERT: I 77 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9095 (pt) REVERT: K 31 MET cc_start: 0.5759 (mpp) cc_final: 0.5165 (mmt) REVERT: J 5 PHE cc_start: 0.3916 (OUTLIER) cc_final: 0.2086 (m-80) REVERT: J 72 MET cc_start: 0.6491 (tpt) cc_final: 0.4137 (ttm) REVERT: J 112 LEU cc_start: 0.6556 (pp) cc_final: 0.6302 (tp) REVERT: J 134 PHE cc_start: 0.6865 (t80) cc_final: 0.6502 (t80) REVERT: A 73 MET cc_start: 0.6840 (tmm) cc_final: 0.6047 (ttt) REVERT: H 311 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5715 (mp) REVERT: M 156 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6383 (tp) REVERT: M 215 MET cc_start: 0.4957 (mmm) cc_final: 0.4419 (mpp) REVERT: M 308 GLN cc_start: 0.4008 (OUTLIER) cc_final: 0.3623 (tp40) REVERT: M 374 MET cc_start: 0.5051 (pmm) cc_final: 0.4655 (pmm) REVERT: M 460 MET cc_start: -0.0243 (OUTLIER) cc_final: -0.1097 (ptt) REVERT: M 462 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5250 (tt) REVERT: M 475 LEU cc_start: 0.7448 (pp) cc_final: 0.6061 (tp) REVERT: L 73 PHE cc_start: 0.4632 (OUTLIER) cc_final: 0.2239 (m-10) REVERT: L 113 TYR cc_start: 0.5370 (p90) cc_final: 0.4781 (p90) REVERT: L 191 GLU cc_start: 0.6186 (tp30) cc_final: 0.5744 (tp30) REVERT: L 214 MET cc_start: 0.1757 (tmm) cc_final: 0.1258 (tmm) REVERT: L 275 MET cc_start: 0.2180 (mmt) cc_final: 0.1330 (mmt) REVERT: L 305 LYS cc_start: 0.5259 (mmtt) cc_final: 0.4026 (mmtt) REVERT: L 306 ARG cc_start: 0.7898 (ptt90) cc_final: 0.6864 (ptt90) REVERT: L 313 MET cc_start: 0.4780 (mtp) cc_final: 0.4372 (mtp) REVERT: L 592 ARG cc_start: 0.4443 (mtt90) cc_final: 0.3163 (ptt90) REVERT: L 598 MET cc_start: 0.6635 (mmp) cc_final: 0.5379 (mmp) REVERT: N 68 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5945 (tpt-90) REVERT: N 74 MET cc_start: 0.5713 (mtp) cc_final: 0.5388 (mmm) REVERT: N 140 PHE cc_start: 0.5611 (m-80) cc_final: 0.4994 (m-10) REVERT: N 151 ARG cc_start: 0.5277 (ptp-170) cc_final: 0.4462 (ttp-110) REVERT: N 174 MET cc_start: 0.7192 (mtt) cc_final: 0.6907 (mtt) REVERT: N 286 LEU cc_start: 0.8212 (mp) cc_final: 0.7857 (mp) REVERT: N 379 MET cc_start: 0.6277 (mmt) cc_final: 0.5214 (mmt) REVERT: N 427 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6851 (mmm160) outliers start: 145 outliers final: 98 residues processed: 1105 average time/residue: 0.2149 time to fit residues: 385.2833 Evaluate side-chains 1116 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1005 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 308 GLN Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 249 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 289 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 114 ASN F 217 ASN G 628 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.240270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.195147 restraints weight = 53709.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199019 restraints weight = 68371.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.197211 restraints weight = 25120.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.197656 restraints weight = 28068.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.197408 restraints weight = 19056.068| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36124 Z= 0.166 Angle : 0.988 59.534 49208 Z= 0.370 Chirality : 0.046 0.452 5554 Planarity : 0.005 0.074 6256 Dihedral : 5.166 88.721 4990 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.37 % Allowed : 25.17 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.12), residues: 4573 helix: 0.61 (0.10), residues: 2527 sheet: -0.81 (0.30), residues: 291 loop : -1.30 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 403 TYR 0.032 0.002 TYR D 264 PHE 0.054 0.002 PHE H 278 TRP 0.041 0.001 TRP L 328 HIS 0.014 0.001 HIS G 653 Details of bonding type rmsd covalent geometry : bond 0.00375 (36088) covalent geometry : angle 0.72345 (49115) hydrogen bonds : bond 0.04238 ( 1899) hydrogen bonds : angle 4.83840 ( 5475) metal coordination : bond 0.01284 ( 36) metal coordination : angle 15.50988 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1038 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7185 (mmp80) cc_final: 0.6935 (mmt180) REVERT: B 113 LEU cc_start: 0.8997 (mp) cc_final: 0.8525 (mp) REVERT: B 170 MET cc_start: 0.8035 (ttp) cc_final: 0.7814 (ttp) REVERT: D 16 HIS cc_start: 0.6175 (m-70) cc_final: 0.5882 (m-70) REVERT: D 63 LEU cc_start: 0.7894 (tp) cc_final: 0.7600 (tt) REVERT: D 150 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7246 (p0) REVERT: D 258 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.7017 (ptm-80) REVERT: D 305 MET cc_start: 0.8131 (ttp) cc_final: 0.7903 (ttp) REVERT: D 392 LYS cc_start: 0.7970 (pttm) cc_final: 0.7441 (mmmt) REVERT: D 497 THR cc_start: 0.9574 (m) cc_final: 0.9269 (p) REVERT: D 532 MET cc_start: 0.7246 (pmm) cc_final: 0.6892 (pmm) REVERT: D 553 TYR cc_start: 0.8226 (t80) cc_final: 0.7548 (t80) REVERT: E 18 GLU cc_start: 0.8448 (mp0) cc_final: 0.8083 (pm20) REVERT: E 60 ASP cc_start: 0.7580 (t0) cc_final: 0.7189 (p0) REVERT: E 103 GLN cc_start: 0.6337 (mp10) cc_final: 0.6076 (mp10) REVERT: F 1 MET cc_start: 0.7252 (ppp) cc_final: 0.2970 (tpp) REVERT: F 30 ARG cc_start: 0.6046 (tpm170) cc_final: 0.5717 (tpm170) REVERT: F 252 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: F 262 TRP cc_start: 0.7711 (m-90) cc_final: 0.7379 (m-90) REVERT: F 358 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7863 (ttp80) REVERT: G 62 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7366 (mtp-110) REVERT: G 159 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7933 (ttp-170) REVERT: G 219 TRP cc_start: 0.8817 (p90) cc_final: 0.8522 (p90) REVERT: G 351 LEU cc_start: 0.7680 (tt) cc_final: 0.6795 (tp) REVERT: G 354 LYS cc_start: 0.7516 (mtpp) cc_final: 0.6951 (ttpt) REVERT: G 361 ILE cc_start: 0.7395 (mm) cc_final: 0.7164 (mt) REVERT: G 367 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.6566 (ttt180) REVERT: G 537 ASN cc_start: 0.8290 (t0) cc_final: 0.7724 (t0) REVERT: G 572 HIS cc_start: 0.7623 (m-70) cc_final: 0.7274 (m90) REVERT: G 597 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6571 (ttm-80) REVERT: G 601 MET cc_start: 0.7550 (mtt) cc_final: 0.7296 (mtt) REVERT: G 835 MET cc_start: 0.6545 (ttt) cc_final: 0.6197 (ttt) REVERT: G 886 MET cc_start: 0.7376 (mmp) cc_final: 0.7165 (mmm) REVERT: K 31 MET cc_start: 0.5581 (mpp) cc_final: 0.5185 (mmt) REVERT: K 57 ASP cc_start: 0.8265 (t0) cc_final: 0.7966 (t0) REVERT: J 5 PHE cc_start: 0.3855 (OUTLIER) cc_final: 0.2045 (m-80) REVERT: J 72 MET cc_start: 0.6302 (tpt) cc_final: 0.3977 (ttm) REVERT: J 112 LEU cc_start: 0.6576 (pp) cc_final: 0.6346 (tp) REVERT: J 134 PHE cc_start: 0.6791 (t80) cc_final: 0.6520 (t80) REVERT: A 73 MET cc_start: 0.6628 (tmm) cc_final: 0.5935 (ttt) REVERT: H 311 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5758 (mp) REVERT: M 156 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5844 (tp) REVERT: M 308 GLN cc_start: 0.4102 (OUTLIER) cc_final: 0.3741 (tp40) REVERT: M 374 MET cc_start: 0.4168 (pmm) cc_final: 0.3659 (pmm) REVERT: M 460 MET cc_start: -0.1147 (OUTLIER) cc_final: -0.1563 (ptt) REVERT: M 462 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5756 (tt) REVERT: L 191 GLU cc_start: 0.5977 (tp30) cc_final: 0.5751 (tp30) REVERT: L 214 MET cc_start: 0.1771 (tmm) cc_final: 0.1494 (tmm) REVERT: L 216 MET cc_start: 0.2723 (mpp) cc_final: 0.2110 (mpp) REVERT: L 275 MET cc_start: 0.2320 (mmt) cc_final: 0.1576 (mmt) REVERT: L 306 ARG cc_start: 0.7772 (ptt90) cc_final: 0.6927 (ppt170) REVERT: L 313 MET cc_start: 0.4386 (mtp) cc_final: 0.4089 (mtp) REVERT: L 319 MET cc_start: 0.5702 (mmm) cc_final: 0.4761 (mmm) REVERT: L 592 ARG cc_start: 0.4762 (mtt90) cc_final: 0.3326 (ptt90) REVERT: L 598 MET cc_start: 0.6553 (mmp) cc_final: 0.5184 (mmp) REVERT: N 68 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.5791 (tpt-90) REVERT: N 74 MET cc_start: 0.5644 (mtp) cc_final: 0.5352 (mmm) REVERT: N 140 PHE cc_start: 0.5055 (m-80) cc_final: 0.4579 (m-10) REVERT: N 174 MET cc_start: 0.7139 (mtt) cc_final: 0.6667 (mtp) REVERT: N 286 LEU cc_start: 0.8069 (mp) cc_final: 0.7745 (mp) REVERT: N 379 MET cc_start: 0.6172 (mmt) cc_final: 0.5185 (mmt) outliers start: 154 outliers final: 121 residues processed: 1103 average time/residue: 0.2169 time to fit residues: 389.2145 Evaluate side-chains 1134 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1002 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 308 GLN Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 460 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 362 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN G 229 GLN G 236 ASN G 628 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.240631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.194552 restraints weight = 53798.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.197885 restraints weight = 68070.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.197061 restraints weight = 24314.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.197700 restraints weight = 18774.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197815 restraints weight = 14483.819| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 36124 Z= 0.160 Angle : 0.939 52.872 49208 Z= 0.374 Chirality : 0.046 0.445 5554 Planarity : 0.005 0.061 6256 Dihedral : 5.082 89.405 4988 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.20 % Allowed : 26.13 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4573 helix: 0.62 (0.10), residues: 2535 sheet: -0.41 (0.31), residues: 263 loop : -1.29 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 403 TYR 0.029 0.002 TYR L 189 PHE 0.060 0.002 PHE L 186 TRP 0.043 0.002 TRP L 328 HIS 0.015 0.001 HIS G 653 Details of bonding type rmsd covalent geometry : bond 0.00359 (36088) covalent geometry : angle 0.73498 (49115) hydrogen bonds : bond 0.04205 ( 1899) hydrogen bonds : angle 4.83869 ( 5475) metal coordination : bond 0.01237 ( 36) metal coordination : angle 13.45363 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1027 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6952 (mmt180) REVERT: D 16 HIS cc_start: 0.6212 (m-70) cc_final: 0.5911 (m-70) REVERT: D 80 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7743 (mp) REVERT: D 258 ARG cc_start: 0.7318 (ptm-80) cc_final: 0.6933 (ptm-80) REVERT: D 391 GLU cc_start: 0.7467 (pt0) cc_final: 0.6965 (pt0) REVERT: D 392 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7450 (mmtm) REVERT: D 497 THR cc_start: 0.9523 (m) cc_final: 0.9273 (p) REVERT: D 532 MET cc_start: 0.7262 (pmm) cc_final: 0.6902 (pmm) REVERT: D 553 TYR cc_start: 0.8237 (t80) cc_final: 0.7547 (t80) REVERT: E 18 GLU cc_start: 0.8415 (mp0) cc_final: 0.7986 (pm20) REVERT: E 60 ASP cc_start: 0.7595 (t0) cc_final: 0.7157 (p0) REVERT: E 103 GLN cc_start: 0.6449 (mp10) cc_final: 0.6111 (mp10) REVERT: E 144 MET cc_start: 0.7431 (ptm) cc_final: 0.6845 (ptm) REVERT: F 1 MET cc_start: 0.7271 (ppp) cc_final: 0.2967 (tpp) REVERT: F 25 TRP cc_start: 0.7571 (m100) cc_final: 0.7137 (m100) REVERT: F 30 ARG cc_start: 0.6109 (tpm170) cc_final: 0.5727 (tpm170) REVERT: F 76 MET cc_start: 0.7792 (mmm) cc_final: 0.7359 (mmm) REVERT: F 94 MET cc_start: 0.6690 (ttm) cc_final: 0.6475 (ttm) REVERT: F 252 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: F 262 TRP cc_start: 0.7667 (m-90) cc_final: 0.7138 (m-90) REVERT: F 338 LEU cc_start: 0.8667 (tp) cc_final: 0.8426 (tp) REVERT: F 358 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: G 62 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7293 (mtp-110) REVERT: G 159 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7838 (ttp-170) REVERT: G 219 TRP cc_start: 0.8793 (p90) cc_final: 0.8466 (p90) REVERT: G 351 LEU cc_start: 0.7670 (tt) cc_final: 0.6742 (tp) REVERT: G 354 LYS cc_start: 0.7288 (mtpp) cc_final: 0.6908 (ttpt) REVERT: G 367 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6587 (ttt180) REVERT: G 537 ASN cc_start: 0.8308 (t0) cc_final: 0.7471 (t0) REVERT: G 572 HIS cc_start: 0.7587 (m-70) cc_final: 0.7241 (m90) REVERT: G 852 VAL cc_start: 0.6613 (OUTLIER) cc_final: 0.6393 (m) REVERT: G 886 MET cc_start: 0.7499 (mmp) cc_final: 0.7273 (mmm) REVERT: I 77 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9112 (pt) REVERT: K 31 MET cc_start: 0.5663 (mpp) cc_final: 0.5345 (mmt) REVERT: K 57 ASP cc_start: 0.8156 (t0) cc_final: 0.7890 (t0) REVERT: J 5 PHE cc_start: 0.3832 (OUTLIER) cc_final: 0.2054 (m-80) REVERT: J 72 MET cc_start: 0.6237 (tpt) cc_final: 0.3992 (ttm) REVERT: J 112 LEU cc_start: 0.6504 (pp) cc_final: 0.6103 (mt) REVERT: J 134 PHE cc_start: 0.6728 (t80) cc_final: 0.6513 (t80) REVERT: A 73 MET cc_start: 0.6569 (tmm) cc_final: 0.5918 (ttt) REVERT: H 88 MET cc_start: 0.4812 (mtp) cc_final: 0.4425 (mmt) REVERT: H 311 ILE cc_start: 0.6029 (OUTLIER) cc_final: 0.5501 (mp) REVERT: M 152 PHE cc_start: 0.6635 (t80) cc_final: 0.6278 (t80) REVERT: M 291 MET cc_start: 0.7720 (mmp) cc_final: 0.6987 (mmp) REVERT: M 374 MET cc_start: 0.4138 (pmm) cc_final: 0.3588 (pmm) REVERT: M 467 MET cc_start: 0.6842 (ptp) cc_final: 0.6354 (ptp) REVERT: L 191 GLU cc_start: 0.5845 (tp30) cc_final: 0.5575 (tp30) REVERT: L 306 ARG cc_start: 0.7747 (ptt90) cc_final: 0.7362 (ppt170) REVERT: L 313 MET cc_start: 0.4410 (mtp) cc_final: 0.4123 (mtp) REVERT: L 319 MET cc_start: 0.6127 (mmm) cc_final: 0.5168 (mmm) REVERT: L 587 GLU cc_start: 0.0808 (tt0) cc_final: 0.0509 (tp30) REVERT: L 592 ARG cc_start: 0.4689 (mtt90) cc_final: 0.3255 (ptt90) REVERT: N 68 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5868 (tpt-90) REVERT: N 74 MET cc_start: 0.5206 (mtp) cc_final: 0.4995 (mmm) REVERT: N 140 PHE cc_start: 0.4954 (m-80) cc_final: 0.4533 (m-10) REVERT: N 174 MET cc_start: 0.7300 (mtt) cc_final: 0.6824 (mtp) REVERT: N 286 LEU cc_start: 0.8074 (mp) cc_final: 0.7766 (mp) REVERT: N 379 MET cc_start: 0.6246 (mmt) cc_final: 0.5171 (mmt) REVERT: N 427 ARG cc_start: 0.6825 (mmm160) cc_final: 0.6354 (mmm160) outliers start: 148 outliers final: 118 residues processed: 1090 average time/residue: 0.2147 time to fit residues: 382.4990 Evaluate side-chains 1140 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1012 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 776 LEU Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 359 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 388 optimal weight: 50.0000 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 420 optimal weight: 7.9990 chunk 220 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN D 279 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN G 229 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 HIS ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.241718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.195575 restraints weight = 53930.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198475 restraints weight = 66689.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198193 restraints weight = 23950.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.198491 restraints weight = 18328.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.198846 restraints weight = 14685.288| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36124 Z= 0.151 Angle : 0.907 44.870 49208 Z= 0.380 Chirality : 0.046 0.489 5554 Planarity : 0.005 0.060 6256 Dihedral : 4.954 89.537 4986 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.11 % Allowed : 26.73 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.23 (0.12), residues: 4573 helix: 0.66 (0.10), residues: 2539 sheet: -0.39 (0.31), residues: 269 loop : -1.27 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 403 TYR 0.027 0.002 TYR L 189 PHE 0.050 0.002 PHE H 282 TRP 0.032 0.001 TRP G 94 HIS 0.012 0.001 HIS L 334 Details of bonding type rmsd covalent geometry : bond 0.00339 (36088) covalent geometry : angle 0.75100 (49115) hydrogen bonds : bond 0.04167 ( 1899) hydrogen bonds : angle 4.81730 ( 5475) metal coordination : bond 0.01056 ( 36) metal coordination : angle 11.73769 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1028 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7143 (mmp80) cc_final: 0.6916 (mmt180) REVERT: B 113 LEU cc_start: 0.8761 (mp) cc_final: 0.8461 (mp) REVERT: D 16 HIS cc_start: 0.6191 (m-70) cc_final: 0.5894 (m-70) REVERT: D 63 LEU cc_start: 0.7902 (tp) cc_final: 0.7515 (tt) REVERT: D 258 ARG cc_start: 0.7216 (ptm-80) cc_final: 0.6798 (ptm-80) REVERT: D 497 THR cc_start: 0.9457 (m) cc_final: 0.9253 (p) REVERT: D 532 MET cc_start: 0.7080 (pmm) cc_final: 0.6750 (pmm) REVERT: D 553 TYR cc_start: 0.8207 (t80) cc_final: 0.7486 (t80) REVERT: E 60 ASP cc_start: 0.7623 (t0) cc_final: 0.7160 (p0) REVERT: E 103 GLN cc_start: 0.6387 (mp10) cc_final: 0.6076 (mp10) REVERT: F 1 MET cc_start: 0.7272 (ppp) cc_final: 0.3042 (tpp) REVERT: F 30 ARG cc_start: 0.6117 (tpm170) cc_final: 0.5720 (tpm170) REVERT: F 49 GLU cc_start: 0.7536 (tp30) cc_final: 0.7090 (tp30) REVERT: F 55 LYS cc_start: 0.8542 (tptt) cc_final: 0.8337 (tppt) REVERT: F 121 PHE cc_start: 0.7298 (t80) cc_final: 0.6942 (t80) REVERT: F 252 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: F 262 TRP cc_start: 0.7605 (m-90) cc_final: 0.6356 (m-90) REVERT: F 338 LEU cc_start: 0.8639 (tp) cc_final: 0.8414 (tp) REVERT: F 358 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7552 (ttp80) REVERT: G 62 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7139 (mtp-110) REVERT: G 159 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7937 (ttp-170) REVERT: G 219 TRP cc_start: 0.8758 (p90) cc_final: 0.8420 (p90) REVERT: G 221 MET cc_start: 0.8474 (mmt) cc_final: 0.8008 (mmm) REVERT: G 354 LYS cc_start: 0.7255 (mtpp) cc_final: 0.6923 (ttpt) REVERT: G 361 ILE cc_start: 0.7838 (mt) cc_final: 0.7575 (mm) REVERT: G 367 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6654 (ttt180) REVERT: G 420 ASN cc_start: 0.8280 (t0) cc_final: 0.7720 (t0) REVERT: G 537 ASN cc_start: 0.8280 (t0) cc_final: 0.7481 (t0) REVERT: G 572 HIS cc_start: 0.7570 (m-70) cc_final: 0.7244 (m90) REVERT: G 597 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6788 (ttm-80) REVERT: G 852 VAL cc_start: 0.6474 (OUTLIER) cc_final: 0.6201 (m) REVERT: I 77 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9095 (pt) REVERT: I 148 TYR cc_start: 0.8137 (t80) cc_final: 0.7549 (t80) REVERT: K 31 MET cc_start: 0.5658 (mpp) cc_final: 0.5386 (mmt) REVERT: K 57 ASP cc_start: 0.8142 (t0) cc_final: 0.7857 (t0) REVERT: K 85 ARG cc_start: 0.7054 (mtt90) cc_final: 0.6664 (mtt90) REVERT: J 5 PHE cc_start: 0.3695 (OUTLIER) cc_final: 0.1945 (m-80) REVERT: J 72 MET cc_start: 0.6383 (tpt) cc_final: 0.4333 (ttm) REVERT: J 112 LEU cc_start: 0.6501 (pp) cc_final: 0.6241 (tp) REVERT: A 73 MET cc_start: 0.6482 (tmm) cc_final: 0.5724 (ttt) REVERT: H 88 MET cc_start: 0.4660 (mtp) cc_final: 0.4371 (mmt) REVERT: H 311 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5509 (mp) REVERT: M 55 THR cc_start: 0.5875 (OUTLIER) cc_final: 0.5612 (t) REVERT: M 152 PHE cc_start: 0.6171 (t80) cc_final: 0.5559 (t80) REVERT: M 323 MET cc_start: 0.7367 (tmm) cc_final: 0.6905 (tmm) REVERT: M 467 MET cc_start: 0.6996 (ptp) cc_final: 0.6609 (ptp) REVERT: L 73 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.5750 (m-10) REVERT: L 243 MET cc_start: 0.3927 (OUTLIER) cc_final: 0.3661 (ttp) REVERT: L 258 MET cc_start: -0.2533 (mmm) cc_final: -0.2881 (mmm) REVERT: L 319 MET cc_start: 0.5508 (mmm) cc_final: 0.4502 (mmm) REVERT: L 592 ARG cc_start: 0.4672 (mtt90) cc_final: 0.3375 (ttp80) REVERT: L 598 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.5330 (mmp) REVERT: N 68 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5850 (tpt-90) REVERT: N 74 MET cc_start: 0.5203 (mtp) cc_final: 0.4969 (mmm) REVERT: N 174 MET cc_start: 0.7262 (mtt) cc_final: 0.6789 (mtp) REVERT: N 286 LEU cc_start: 0.8142 (mp) cc_final: 0.7768 (mp) REVERT: N 379 MET cc_start: 0.6211 (mmt) cc_final: 0.5166 (mmt) REVERT: N 427 ARG cc_start: 0.6826 (mmm160) cc_final: 0.6320 (mmm160) outliers start: 145 outliers final: 115 residues processed: 1091 average time/residue: 0.2154 time to fit residues: 382.2332 Evaluate side-chains 1126 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 999 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 776 LEU Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 248 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 34 optimal weight: 4.9990 chunk 443 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 359 optimal weight: 40.0000 chunk 201 optimal weight: 0.0010 chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN G 229 GLN G 236 ASN G 653 HIS ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 135 ASN L 207 HIS N 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.236739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.190218 restraints weight = 53591.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.193438 restraints weight = 69798.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192627 restraints weight = 25651.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.192413 restraints weight = 27646.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192446 restraints weight = 20791.379| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 36124 Z= 0.255 Angle : 1.078 62.188 49208 Z= 0.429 Chirality : 0.051 0.548 5554 Planarity : 0.006 0.072 6256 Dihedral : 5.330 88.084 4986 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.00 % Allowed : 27.32 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4573 helix: 0.49 (0.10), residues: 2533 sheet: -0.74 (0.30), residues: 265 loop : -1.41 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 403 TYR 0.032 0.002 TYR M 207 PHE 0.051 0.002 PHE H 132 TRP 0.052 0.002 TRP G 94 HIS 0.014 0.002 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00576 (36088) covalent geometry : angle 0.83226 (49115) hydrogen bonds : bond 0.04801 ( 1899) hydrogen bonds : angle 5.08899 ( 5475) metal coordination : bond 0.02064 ( 36) metal coordination : angle 15.76705 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1008 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7303 (mmp80) cc_final: 0.7029 (mmt180) REVERT: B 113 LEU cc_start: 0.8869 (mp) cc_final: 0.8654 (mt) REVERT: D 264 TYR cc_start: 0.8508 (t80) cc_final: 0.8290 (t80) REVERT: D 497 THR cc_start: 0.9563 (m) cc_final: 0.9194 (p) REVERT: D 532 MET cc_start: 0.7210 (pmm) cc_final: 0.6903 (pmm) REVERT: D 553 TYR cc_start: 0.8260 (t80) cc_final: 0.7474 (t80) REVERT: E 23 GLU cc_start: 0.7267 (pp20) cc_final: 0.7064 (pp20) REVERT: E 44 GLN cc_start: 0.9098 (tt0) cc_final: 0.8825 (tt0) REVERT: E 103 GLN cc_start: 0.6644 (mp10) cc_final: 0.6349 (mp10) REVERT: F 1 MET cc_start: 0.7432 (ppp) cc_final: 0.3221 (tpp) REVERT: F 55 LYS cc_start: 0.8541 (tptt) cc_final: 0.8339 (tppt) REVERT: F 121 PHE cc_start: 0.7428 (t80) cc_final: 0.7076 (t80) REVERT: F 252 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: F 262 TRP cc_start: 0.7750 (m-90) cc_final: 0.7489 (m-90) REVERT: F 338 LEU cc_start: 0.8753 (tp) cc_final: 0.8535 (tp) REVERT: F 358 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.7624 (ttp80) REVERT: G 159 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7870 (ttp-170) REVERT: G 219 TRP cc_start: 0.8895 (p90) cc_final: 0.8608 (p90) REVERT: G 221 MET cc_start: 0.8855 (mmt) cc_final: 0.8092 (mmm) REVERT: G 293 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7950 (mt) REVERT: G 351 LEU cc_start: 0.7782 (tt) cc_final: 0.7066 (tp) REVERT: G 354 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7476 (ttpt) REVERT: G 367 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6697 (ttt180) REVERT: G 537 ASN cc_start: 0.8386 (t0) cc_final: 0.7584 (t0) REVERT: G 551 GLU cc_start: 0.7184 (pp20) cc_final: 0.6858 (pp20) REVERT: G 572 HIS cc_start: 0.7810 (m-70) cc_final: 0.7300 (m170) REVERT: G 852 VAL cc_start: 0.6851 (OUTLIER) cc_final: 0.6583 (m) REVERT: G 886 MET cc_start: 0.7827 (mmp) cc_final: 0.7458 (mmm) REVERT: I 77 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9146 (pt) REVERT: K 57 ASP cc_start: 0.8258 (t0) cc_final: 0.8042 (t0) REVERT: K 85 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6711 (mtt90) REVERT: J 5 PHE cc_start: 0.4150 (OUTLIER) cc_final: 0.2230 (m-80) REVERT: J 72 MET cc_start: 0.5936 (tpt) cc_final: 0.3879 (ttm) REVERT: J 112 LEU cc_start: 0.6658 (pp) cc_final: 0.6448 (tp) REVERT: H 310 LEU cc_start: 0.6331 (mt) cc_final: 0.5821 (mt) REVERT: H 311 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.5717 (mp) REVERT: M 36 MET cc_start: 0.2945 (tmm) cc_final: 0.2328 (tmm) REVERT: M 152 PHE cc_start: 0.6112 (t80) cc_final: 0.5524 (t80) REVERT: M 211 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.3876 (pp) REVERT: M 291 MET cc_start: 0.7396 (mmp) cc_final: 0.6834 (mmp) REVERT: M 323 MET cc_start: 0.6414 (tmm) cc_final: 0.5774 (tmm) REVERT: M 373 MET cc_start: 0.6884 (mpp) cc_final: 0.5420 (ptp) REVERT: M 460 MET cc_start: -0.0444 (ptm) cc_final: -0.1458 (ttp) REVERT: L 73 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.6038 (m-10) REVERT: L 258 MET cc_start: -0.2810 (mmm) cc_final: -0.3060 (mmm) REVERT: L 275 MET cc_start: 0.1923 (mmt) cc_final: 0.0699 (mpp) REVERT: L 319 MET cc_start: 0.5420 (mmm) cc_final: 0.4312 (mmm) REVERT: L 592 ARG cc_start: 0.5144 (mtt90) cc_final: 0.3484 (ptt180) REVERT: L 598 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.5711 (mmp) REVERT: N 16 ILE cc_start: 0.7431 (tp) cc_final: 0.7168 (pt) REVERT: N 68 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.5897 (tpt-90) REVERT: N 74 MET cc_start: 0.5675 (mtp) cc_final: 0.5309 (mmm) REVERT: N 151 ARG cc_start: 0.5246 (ptp-170) cc_final: 0.4819 (ttp-110) REVERT: N 174 MET cc_start: 0.7395 (mtt) cc_final: 0.7010 (mtp) REVERT: N 286 LEU cc_start: 0.8113 (mp) cc_final: 0.7713 (mp) REVERT: N 379 MET cc_start: 0.6210 (mmt) cc_final: 0.5223 (mmt) REVERT: N 427 ARG cc_start: 0.6898 (mmm160) cc_final: 0.6375 (mmm160) outliers start: 141 outliers final: 117 residues processed: 1069 average time/residue: 0.2118 time to fit residues: 368.2225 Evaluate side-chains 1123 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 994 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 653 HIS Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 0.5980 chunk 280 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 chunk 361 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 210 optimal weight: 0.0470 chunk 396 optimal weight: 0.0030 chunk 263 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN D 472 GLN D 482 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN G 54 GLN G 111 ASN G 236 ASN G 653 HIS ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.242136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.196273 restraints weight = 53819.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200146 restraints weight = 68377.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199066 restraints weight = 23967.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.199070 restraints weight = 26930.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.199115 restraints weight = 18764.699| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36124 Z= 0.149 Angle : 0.928 45.448 49208 Z= 0.394 Chirality : 0.047 0.543 5554 Planarity : 0.005 0.064 6256 Dihedral : 5.041 89.981 4986 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.23 % Allowed : 28.68 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4573 helix: 0.65 (0.10), residues: 2528 sheet: -0.48 (0.31), residues: 263 loop : -1.30 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 403 TYR 0.032 0.002 TYR M 207 PHE 0.054 0.002 PHE H 282 TRP 0.047 0.002 TRP G 94 HIS 0.009 0.001 HIS L 334 Details of bonding type rmsd covalent geometry : bond 0.00329 (36088) covalent geometry : angle 0.78479 (49115) hydrogen bonds : bond 0.04209 ( 1899) hydrogen bonds : angle 4.91541 ( 5475) metal coordination : bond 0.00802 ( 36) metal coordination : angle 11.41440 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8410.41 seconds wall clock time: 144 minutes 30.69 seconds (8670.69 seconds total)