Starting phenix.real_space_refine on Mon Jul 6 11:22:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nyr_12653/07_2026/7nyr_12653.map" } resolution = 3.3 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 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 158 176.319 106.819 74.265 1.00 26.83 S ATOM 181 SG CYS B 64 173.867 100.719 74.407 1.00 47.89 S ATOM 175 SG CYS B 63 170.823 104.024 71.208 1.00 53.71 S ATOM 593 SG CYS B 129 171.254 107.059 75.960 1.00 18.29 S ATOM 6594 SG CYS E 92 223.185 162.563 69.448 1.00 26.86 S ATOM 6628 SG CYS E 97 225.902 162.513 67.542 1.00 21.17 S ATOM 6907 SG CYS E 133 220.259 166.128 67.741 1.00 28.24 S ATOM 6933 SG CYS E 137 221.922 166.701 65.917 1.00 26.53 S ATOM 9934 SG CYS F 357 203.697 156.760 68.879 1.00 44.36 S ATOM 9914 SG CYS F 354 198.836 157.055 69.728 1.00 44.74 S ATOM 10255 SG CYS F 398 201.386 162.796 68.756 1.00 23.05 S ATOM 9890 SG CYS F 351 202.010 160.503 74.285 1.00 15.22 S ATOM 10951 SG CYS G 48 186.193 155.118 68.949 1.00 13.42 S ATOM 11100 SG CYS G 67 186.230 157.903 71.472 1.00 14.30 S ATOM 10849 SG CYS G 34 189.082 155.466 74.510 1.00 28.07 S ATOM 10925 SG CYS G 45 189.738 152.721 72.490 1.00 42.19 S ATOM 11831 SG CYS G 157 194.027 152.540 85.378 1.00 28.19 S ATOM 11783 SG CYS G 151 197.390 148.655 81.608 1.00 24.56 S ATOM 11802 SG CYS G 154 191.342 150.738 80.022 1.00 20.46 S ATOM 12179 SG CYS G 201 191.568 146.570 84.269 1.00 4.08 S ATOM 11408 SG CYS G 106 192.484 137.300 83.778 1.00 11.66 S ATOM 11388 SG CYS G 103 192.941 134.531 78.073 1.00 30.01 S ATOM 11448 SG CYS G 112 189.288 140.217 79.397 1.00 7.96 S ATOM 12428 SG CYS G 231 173.947 152.855 102.383 1.00 5.72 S ATOM 12452 SG CYS G 235 173.951 151.957 96.363 1.00 21.99 S ATOM 12404 SG CYS G 228 174.521 147.630 99.933 1.00 12.19 S ATOM 12689 SG CYS G 263 179.215 151.559 99.495 1.00 32.96 S ATOM 18292 SG CYS I 109 192.679 120.424 80.024 1.00 14.30 S ATOM 17915 SG CYS I 60 192.123 120.636 86.718 1.00 14.04 S ATOM 17955 SG CYS I 66 186.942 120.154 83.100 1.00 9.56 S ATOM 17933 SG CYS I 63 190.189 125.202 82.059 1.00 22.65 S ATOM 17978 SG CYS I 70 179.732 116.768 80.012 1.00 12.73 S ATOM 18245 SG CYS I 102 181.395 114.427 74.967 1.00 13.79 S ATOM 18220 SG CYS I 99 181.995 110.303 80.167 1.00 12.53 S ATOM 18263 SG CYS I 105 185.971 115.032 78.523 1.00 12.24 S Time building chain proxies: 7.35, per 1000 atoms: 0.21 Number of scatterers: 35228 At special positions: 0 Unit cell: (253.339, 211.694, 144.6, 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " 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="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb=" SF4 G1004 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 228 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " 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: 207 helices and 26 sheets defined 60.4% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.545A pdb=" N SER B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.937A pdb=" N MET B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.540A pdb=" N ILE B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.551A pdb=" N LYS B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.738A pdb=" N LYS B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.605A 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 52 through 62 Processing helix chain 'D' and resid 129 through 141 removed outlier: 4.112A 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: 3.611A pdb=" N LYS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 removed outlier: 3.807A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.853A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 292 removed outlier: 3.558A 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 Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.972A pdb=" N THR D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 396 removed outlier: 3.700A 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: 3.552A 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 567 removed outlier: 4.266A pdb=" N ALA D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 572 removed outlier: 3.791A pdb=" N ALA D 571 " --> pdb=" O GLN D 567 " (cutoff:3.500A) 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 51 through 63 removed outlier: 3.966A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.026A 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: 3.785A pdb=" N TYR E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 removed outlier: 3.577A pdb=" N SER F 31 " --> pdb=" O ASP F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.507A pdb=" N GLY F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.095A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.842A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.552A pdb=" N ALA F 140 " --> pdb=" O TYR F 136 " (cutoff:3.500A) 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: 3.903A 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: 3.931A pdb=" N ASN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.612A 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: 3.583A 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 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.761A 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: 3.965A 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: 3.597A pdb=" N GLU G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.524A 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: 3.532A 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: 3.549A 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: 3.558A 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: 4.043A 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: 3.612A pdb=" N GLU G 602 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 616 removed outlier: 3.562A 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 removed outlier: 3.592A pdb=" N VAL G 672 " --> pdb=" O GLN G 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 689 removed outlier: 5.157A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 769 removed outlier: 3.717A pdb=" N GLN G 769 " --> pdb=" O ASN G 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 824 through 829 Proline residue: G 829 - end of helix Processing helix chain 'G' and resid 830 through 835 removed outlier: 4.152A pdb=" N ARG G 834 " --> pdb=" O VAL G 830 " (cutoff:3.500A) 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: 3.596A pdb=" N VAL I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.130A pdb=" N MET I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 25 removed outlier: 4.212A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 53 removed outlier: 3.890A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.735A pdb=" N TYR K 62 " --> pdb=" O GLY K 58 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.924A 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: 3.569A pdb=" N ALA J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 removed outlier: 4.205A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 removed outlier: 3.987A pdb=" N ASN J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 removed outlier: 3.524A pdb=" N ARG J 85 " --> pdb=" O ILE J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 112 removed outlier: 3.697A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.846A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 133 removed outlier: 4.085A pdb=" N VAL J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 159 removed outlier: 3.672A 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: 3.763A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.058A 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: 4.342A 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: 3.634A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 removed outlier: 3.770A 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 126 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.935A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.972A 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: 4.326A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.619A 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: 4.391A 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: 3.729A pdb=" N LEU H 308 " --> pdb=" O ILE H 304 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.167A pdb=" N TRP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 3.523A 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: 3.885A 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: 3.821A 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: 3.765A 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: 4.471A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 262 removed outlier: 3.780A 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: 3.805A 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: 4.271A 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: 3.514A 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: 4.102A 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: 4.132A 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: 6.991A pdb=" N ALA M 453 " --> pdb=" O SER M 450 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) removed outlier: 4.099A 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: 5.119A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.232A 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: 4.014A 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: 4.002A pdb=" N PHE L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 removed outlier: 3.801A 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: 3.574A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) removed outlier: 3.932A 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: 4.485A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.836A 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: 4.032A pdb=" N MET L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.825A 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: 3.566A 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: 3.550A pdb=" N LEU L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.979A 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: 3.646A pdb=" N HIS L 357 " --> pdb=" O ILE L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 removed outlier: 4.022A 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: 4.348A pdb=" N PHE L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.806A 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: 3.674A 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: 3.657A 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: 3.590A pdb=" N GLY N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 58 removed outlier: 4.104A 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: 3.584A 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: 3.697A 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: 3.972A 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: 3.653A 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: 3.825A 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: 3.679A 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: 4.867A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.959A 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: 3.523A pdb=" N PHE B 59 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B 99 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 47 removed outlier: 6.579A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.467A 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: 3.573A pdb=" N VAL D 120 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 212 through 214 removed outlier: 3.901A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.427A 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 527 through 534 Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.703A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.135A 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: 6.576A pdb=" N LEU F 87 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE F 131 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS F 89 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 265 removed outlier: 7.581A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.530A 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: 8.896A pdb=" N ILE G 77 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS G 5 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.264A 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: 8.337A pdb=" N ASN G 236 " --> pdb=" O ASN G 251 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN G 251 " --> pdb=" O ASN G 236 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER G 238 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE G 249 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 6.830A 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: 6.637A pdb=" N VAL G 590 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU G 608 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL G 592 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 564 " --> pdb=" O MET G 591 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL G 593 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 566 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE G 313 " --> pdb=" O VAL G 565 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU G 567 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE G 315 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TYR G 338 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 6.360A 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: 6.388A pdb=" N ALA G 374 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE G 499 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU G 376 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY G 501 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.302A 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: 3.501A 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: 6.715A 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 881 through 885 removed outlier: 6.410A pdb=" N ARG G 811 " --> pdb=" O VAL G 882 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU G 884 " --> pdb=" O ARG G 811 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA G 813 " --> pdb=" O LEU G 884 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 840 through 842 removed outlier: 5.918A pdb=" N ILE G 840 " --> pdb=" O GLU G 872 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.824A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 65 through 66 removed outlier: 4.050A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AC7, 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: 7.587A 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: 5.632A pdb=" N PHE L 77 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 61 through 62 1911 hydrogen bonds defined for protein. 5502 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: 8.50 Time building geometry restraints manager: 4.30 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: 15349 1.43 - 1.65: 20281 1.65 - 1.86: 366 1.86 - 2.08: 0 2.08 - 2.29: 92 Bond restraints: 36088 Sorted by residual: 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 1.34e+01 bond pdb=" CB CSX B 102 " pdb=" SG CSX B 102 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N CSX F 215 " pdb=" CA CSX F 215 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.49e+00 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 46254 1.70 - 3.40: 2348 3.40 - 5.10: 423 5.10 - 6.80: 78 6.80 - 8.50: 12 Bond angle restraints: 49115 Sorted by residual: angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.46 4.91 1.34e+00 5.57e-01 1.34e+01 angle pdb=" C TYR D 343 " pdb=" N ASP D 344 " pdb=" CA ASP D 344 " ideal model delta sigma weight residual 120.72 115.03 5.69 1.67e+00 3.59e-01 1.16e+01 angle pdb=" C LYS D 341 " pdb=" N ILE D 342 " pdb=" CA ILE D 342 " ideal model delta sigma weight residual 120.42 115.71 4.71 1.42e+00 4.96e-01 1.10e+01 angle pdb=" CA PHE L 341 " pdb=" CB PHE L 341 " pdb=" CG PHE L 341 " ideal model delta sigma weight residual 113.80 117.08 -3.28 1.00e+00 1.00e+00 1.08e+01 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 20672 34.08 - 68.15: 401 68.15 - 102.23: 29 102.23 - 136.31: 0 136.31 - 170.39: 1 Dihedral angle restraints: 21103 sinusoidal: 7915 harmonic: 13188 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.21 170.39 1 2.00e+01 2.50e-03 4.77e+01 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 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+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 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 21100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4320 0.054 - 0.108: 1041 0.108 - 0.162: 176 0.162 - 0.216: 14 0.216 - 0.270: 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 2.24 0.27 2.00e-01 2.50e+01 1.83e+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 -0.23 2.00e-01 2.50e+01 1.38e+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 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5551 not shown) Planarity restraints: 6255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C LEU G 457 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU G 457 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY G 458 " 0.026 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 2.34e-02 1.36e+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 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 342 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE D 342 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE D 342 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR D 343 " 0.020 2.00e-02 2.50e+03 ... (remaining 6252 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1279 2.71 - 3.26: 35816 3.26 - 3.80: 57484 3.80 - 4.35: 73812 4.35 - 4.90: 122921 Nonbonded interactions: 291312 Sorted by model distance: nonbonded pdb=" OE2 GLU G 624 " pdb=" NH2 ARG G 784 " model vdw 2.160 3.120 nonbonded pdb=" OE2 GLU D 347 " pdb=" NH1 ARG D 353 " model vdw 2.197 3.120 nonbonded pdb=" CE2 PHE J 156 " pdb=" OE2 GLU N 104 " model vdw 2.200 3.340 nonbonded pdb=" OG SER D 100 " pdb=" OD1 ASP D 102 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.218 3.120 ... (remaining 291307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 39.980 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 0.122 36124 Z= 0.231 Angle : 1.246 52.596 49208 Z= 0.469 Chirality : 0.047 0.270 5554 Planarity : 0.007 0.087 6255 Dihedral : 14.050 170.385 12663 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.82 % Allowed : 2.95 % Favored : 96.23 % 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: -1.75 (0.11), residues: 4573 helix: -0.98 (0.09), residues: 2471 sheet: -0.47 (0.29), residues: 307 loop : -1.34 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 172 TYR 0.054 0.003 TYR N 397 PHE 0.045 0.003 PHE N 396 TRP 0.062 0.002 TRP M 30 HIS 0.014 0.002 HIS G 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (36088) covalent geometry : angle 0.87117 / 0.46 (49115) hydrogen bonds : bond 0.18192 / 12.25 ( 1909) hydrogen bonds : angle 6.87136 / 4.77 ( 5502) metal coordination : bond 0.03919 / 2.52 ( 36) metal coordination : angle 20.51001 / 15.54 ( 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 1212 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1183 time to evaluate : 1.322 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: B 146 ASP cc_start: 0.7339 (p0) cc_final: 0.6924 (p0) REVERT: D 107 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8162 (tp) REVERT: D 305 MET cc_start: 0.7588 (ttp) cc_final: 0.7367 (ttp) REVERT: D 353 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6947 (mtp85) REVERT: E 144 MET cc_start: 0.7974 (mtp) cc_final: 0.6633 (mtp) REVERT: F 388 CYS cc_start: 0.6546 (m) cc_final: 0.6342 (m) REVERT: G 551 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6586 (mp0) REVERT: G 810 TRP cc_start: 0.8387 (m100) cc_final: 0.8165 (m100) REVERT: G 871 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7871 (p) REVERT: I 84 ASP cc_start: 0.6392 (t0) cc_final: 0.5195 (t0) REVERT: K 98 MET cc_start: 0.2269 (ptt) cc_final: 0.1674 (mtt) REVERT: H 121 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5514 (tmm) REVERT: H 232 MET cc_start: 0.4106 (ptm) cc_final: 0.3752 (tpt) REVERT: H 265 LEU cc_start: 0.0897 (pp) cc_final: 0.0603 (pt) REVERT: M 103 LEU cc_start: 0.7036 (mt) cc_final: 0.6802 (mt) REVERT: M 289 ILE cc_start: 0.5862 (mp) cc_final: 0.5659 (mp) REVERT: M 396 LEU cc_start: 0.1560 (pt) cc_final: 0.1072 (tp) REVERT: L 168 MET cc_start: 0.4938 (mpp) cc_final: 0.3411 (ptt) REVERT: L 191 GLU cc_start: 0.3707 (tp30) cc_final: 0.3288 (tp30) REVERT: L 246 PRO cc_start: 0.5137 (Cg_exo) cc_final: 0.4606 (Cg_endo) REVERT: L 329 ASP cc_start: 0.1441 (m-30) cc_final: 0.0015 (m-30) REVERT: N 107 LEU cc_start: 0.6960 (tp) cc_final: 0.6722 (tp) REVERT: N 250 ILE cc_start: 0.7442 (mt) cc_final: 0.7234 (mt) REVERT: N 298 LEU cc_start: 0.4837 (mt) cc_final: 0.4228 (mt) REVERT: N 379 MET cc_start: 0.5328 (mmt) cc_final: 0.5094 (mmt) REVERT: N 380 MET cc_start: 0.5044 (tpp) cc_final: 0.4742 (tpp) outliers start: 29 outliers final: 7 residues processed: 1204 average time/residue: 0.2186 time to fit residues: 429.1650 Evaluate side-chains 980 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 970 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain G residue 527 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain N residue 187 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 50.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN D 397 ASN D 527 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 304 HIS F 434 ASN G 52 GLN G 111 ASN G 454 GLN G 537 ASN G 899 HIS H 188 ASN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 HIS ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.259470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204471 restraints weight = 46839.312| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.43 r_work: 0.3641 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2462 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= 0.184 Angle : 0.833 45.621 49208 Z= 0.356 Chirality : 0.045 0.246 5554 Planarity : 0.005 0.068 6255 Dihedral : 5.886 174.291 5004 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.27 % Allowed : 12.47 % Favored : 85.26 % 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: -0.66 (0.12), residues: 4573 helix: 0.11 (0.10), residues: 2524 sheet: -0.18 (0.30), residues: 281 loop : -1.18 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 30 TYR 0.033 0.002 TYR M 435 PHE 0.032 0.002 PHE N 341 TRP 0.034 0.002 TRP M 18 HIS 0.009 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (36088) covalent geometry : angle 0.68626 / 0.35 (49115) hydrogen bonds : bond 0.05057 / 3.36 ( 1909) hydrogen bonds : angle 4.97625 / 3.45 ( 5502) metal coordination : bond 0.01362 / 0.76 ( 36) metal coordination : angle 10.86832 / 8.11 ( 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 1103 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1023 time to evaluate : 1.180 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: D 26 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7516 (mmt-90) REVERT: D 67 TYR cc_start: 0.8502 (m-80) cc_final: 0.8215 (m-80) REVERT: D 392 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7398 (pttm) REVERT: D 417 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: D 444 GLU cc_start: 0.8611 (pm20) cc_final: 0.8389 (pm20) REVERT: E 148 ASP cc_start: 0.8167 (t0) cc_final: 0.7808 (t0) REVERT: F 35 TYR cc_start: 0.7798 (m-80) cc_final: 0.7262 (m-80) REVERT: F 144 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8114 (mtt-85) REVERT: G 173 TYR cc_start: 0.8661 (m-80) cc_final: 0.8228 (m-80) REVERT: G 264 ASP cc_start: 0.7473 (m-30) cc_final: 0.7233 (m-30) REVERT: G 494 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7970 (mmmt) REVERT: G 537 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (t0) REVERT: G 551 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7458 (mp0) REVERT: G 562 ASP cc_start: 0.7164 (t0) cc_final: 0.6714 (t0) REVERT: G 725 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7768 (ttt180) REVERT: G 886 MET cc_start: 0.8868 (mmm) cc_final: 0.8589 (mmt) REVERT: G 904 LYS cc_start: 0.7908 (pptt) cc_final: 0.7584 (pptt) REVERT: I 133 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7436 (mm-30) REVERT: K 31 MET cc_start: 0.7093 (mpp) cc_final: 0.6533 (mpp) REVERT: K 98 MET cc_start: 0.2381 (ptt) cc_final: 0.2083 (mtt) REVERT: J 64 MET cc_start: 0.4974 (mmm) cc_final: 0.4662 (tpt) REVERT: J 146 MET cc_start: 0.5731 (mtp) cc_final: 0.5400 (mtp) REVERT: H 121 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.4327 (tmm) REVERT: H 132 PHE cc_start: 0.6621 (m-80) cc_final: 0.6390 (m-80) REVERT: H 232 MET cc_start: 0.5096 (ptm) cc_final: 0.4012 (tpt) REVERT: H 280 MET cc_start: 0.7927 (mmp) cc_final: 0.7596 (mmp) REVERT: H 282 PHE cc_start: 0.8723 (m-10) cc_final: 0.8499 (m-10) REVERT: M 48 LEU cc_start: 0.8594 (tt) cc_final: 0.7588 (mt) REVERT: M 67 PHE cc_start: 0.1714 (t80) cc_final: 0.1474 (t80) REVERT: M 103 LEU cc_start: 0.8570 (mt) cc_final: 0.8220 (mt) REVERT: M 128 ILE cc_start: 0.5428 (mt) cc_final: 0.4748 (mm) REVERT: M 131 PHE cc_start: 0.6884 (m-80) cc_final: 0.6610 (m-80) REVERT: M 205 PHE cc_start: 0.5140 (m-10) cc_final: 0.4905 (m-80) REVERT: M 381 MET cc_start: 0.5993 (ptt) cc_final: 0.4409 (ptt) REVERT: M 411 LEU cc_start: 0.4016 (mt) cc_final: 0.3258 (tt) REVERT: M 460 MET cc_start: 0.0156 (pmm) cc_final: -0.0208 (pmm) REVERT: L 74 ASN cc_start: 0.7957 (p0) cc_final: 0.7542 (m-40) REVERT: L 97 PHE cc_start: 0.8399 (t80) cc_final: 0.8185 (t80) REVERT: L 168 MET cc_start: 0.3240 (mpp) cc_final: 0.2013 (ptm) REVERT: L 207 HIS cc_start: 0.6481 (t70) cc_final: 0.6249 (t70) REVERT: N 40 LEU cc_start: 0.9314 (mp) cc_final: 0.9074 (pp) REVERT: N 68 ARG cc_start: 0.6322 (tpp80) cc_final: 0.6004 (ttm110) REVERT: N 92 TYR cc_start: 0.4991 (t80) cc_final: 0.4616 (t80) REVERT: N 123 ASN cc_start: -0.1065 (t0) cc_final: -0.1334 (t0) REVERT: N 130 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6227 (mt) REVERT: N 159 TYR cc_start: 0.6808 (t80) cc_final: 0.6460 (t80) REVERT: N 162 LEU cc_start: 0.5666 (mt) cc_final: 0.5287 (mt) REVERT: N 203 LEU cc_start: 0.5028 (tp) cc_final: 0.4625 (pp) REVERT: N 256 ARG cc_start: 0.6637 (mmm160) cc_final: 0.6370 (mmm160) REVERT: N 258 PHE cc_start: 0.7121 (t80) cc_final: 0.6725 (t80) REVERT: N 283 PHE cc_start: 0.5760 (m-80) cc_final: 0.5194 (m-80) REVERT: N 341 PHE cc_start: 0.6324 (m-80) cc_final: 0.6113 (m-80) REVERT: N 376 MET cc_start: 0.8892 (tpp) cc_final: 0.8679 (tpp) REVERT: N 379 MET cc_start: 0.8046 (mmt) cc_final: 0.6779 (mmt) REVERT: N 380 MET cc_start: 0.6922 (tpp) cc_final: 0.6040 (tpp) REVERT: N 392 PHE cc_start: 0.7088 (t80) cc_final: 0.6703 (t80) REVERT: N 425 TYR cc_start: 0.7298 (m-80) cc_final: 0.6799 (m-80) outliers start: 80 outliers final: 46 residues processed: 1056 average time/residue: 0.2191 time to fit residues: 375.3579 Evaluate side-chains 1018 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 967 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 529 SER Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 595 VAL Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 181 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 35 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 152 optimal weight: 0.2980 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 373 optimal weight: 50.0000 chunk 205 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 397 ASN D 527 ASN F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** G 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 ASN K 40 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 293 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.255794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.201778 restraints weight = 46276.314| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.16 r_work: 0.3609 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 36124 Z= 0.178 Angle : 0.790 44.854 49208 Z= 0.340 Chirality : 0.044 0.244 5554 Planarity : 0.005 0.085 6255 Dihedral : 5.637 173.531 4994 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.06 % Allowed : 15.93 % Favored : 81.01 % 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: -0.20 (0.12), residues: 4573 helix: 0.56 (0.10), residues: 2544 sheet: -0.07 (0.30), residues: 281 loop : -1.10 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 30 TYR 0.032 0.002 TYR L 151 PHE 0.030 0.002 PHE L 341 TRP 0.023 0.001 TRP F 25 HIS 0.013 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (36088) covalent geometry : angle 0.66852 / 0.34 (49115) hydrogen bonds : bond 0.04489 / 2.98 ( 1909) hydrogen bonds : angle 4.77110 / 3.31 ( 5502) metal coordination : bond 0.01544 / 0.84 ( 36) metal coordination : angle 9.70069 / 7.25 ( 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 1085 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 977 time to evaluate : 1.259 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 55 TRP cc_start: 0.7165 (m-90) cc_final: 0.6825 (m-90) REVERT: D 26 ARG cc_start: 0.8102 (mmt180) cc_final: 0.7513 (mmt-90) REVERT: D 374 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7178 (ptp90) REVERT: D 392 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7434 (pttm) REVERT: D 527 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7742 (t0) REVERT: E 60 ASP cc_start: 0.8061 (m-30) cc_final: 0.7674 (m-30) REVERT: E 148 ASP cc_start: 0.8203 (t0) cc_final: 0.7820 (t0) REVERT: F 35 TYR cc_start: 0.7847 (m-80) cc_final: 0.7331 (m-80) REVERT: F 144 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8081 (mtt-85) REVERT: G 173 TYR cc_start: 0.8647 (m-80) cc_final: 0.8343 (m-80) REVERT: G 494 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7993 (mmmt) REVERT: G 537 ASN cc_start: 0.9201 (t0) cc_final: 0.8993 (t0) REVERT: G 551 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7356 (mp0) REVERT: G 886 MET cc_start: 0.8963 (mmm) cc_final: 0.8756 (mmt) REVERT: G 904 LYS cc_start: 0.7827 (pptt) cc_final: 0.7529 (pptt) REVERT: I 84 ASP cc_start: 0.7354 (t0) cc_final: 0.6914 (t0) REVERT: K 31 MET cc_start: 0.7286 (mpp) cc_final: 0.7035 (mpp) REVERT: K 53 TRP cc_start: 0.8268 (m100) cc_final: 0.7655 (m100) REVERT: K 98 MET cc_start: 0.2671 (ptt) cc_final: 0.2255 (ptp) REVERT: J 64 MET cc_start: 0.4893 (mmm) cc_final: 0.4605 (tpt) REVERT: J 146 MET cc_start: 0.5752 (mtp) cc_final: 0.5373 (mtp) REVERT: H 121 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4129 (tmm) REVERT: H 132 PHE cc_start: 0.6568 (m-80) cc_final: 0.6206 (m-80) REVERT: H 174 PHE cc_start: 0.3784 (m-10) cc_final: 0.3514 (m-80) REVERT: H 232 MET cc_start: 0.4911 (ptm) cc_final: 0.3747 (tpt) REVERT: H 280 MET cc_start: 0.7667 (mmp) cc_final: 0.7301 (mmp) REVERT: M 93 LEU cc_start: 0.8500 (tp) cc_final: 0.8290 (tp) REVERT: M 103 LEU cc_start: 0.8602 (mt) cc_final: 0.8231 (mt) REVERT: M 112 TYR cc_start: 0.6945 (p90) cc_final: 0.5427 (p90) REVERT: M 128 ILE cc_start: 0.5554 (mt) cc_final: 0.4853 (mm) REVERT: M 143 TRP cc_start: 0.6035 (t-100) cc_final: 0.5786 (t-100) REVERT: M 186 LEU cc_start: 0.7731 (tp) cc_final: 0.7496 (tp) REVERT: M 210 LEU cc_start: 0.6981 (mt) cc_final: 0.6194 (tp) REVERT: M 222 LEU cc_start: 0.8514 (pp) cc_final: 0.8112 (mp) REVERT: M 223 LEU cc_start: 0.8919 (mp) cc_final: 0.8500 (mp) REVERT: M 224 MET cc_start: 0.6450 (ttt) cc_final: 0.6093 (ttm) REVERT: M 274 PHE cc_start: 0.8119 (m-80) cc_final: 0.7434 (m-80) REVERT: M 336 LEU cc_start: 0.8433 (tp) cc_final: 0.7756 (mp) REVERT: M 381 MET cc_start: 0.4381 (ptt) cc_final: 0.3661 (ptt) REVERT: M 408 PHE cc_start: 0.8573 (t80) cc_final: 0.8319 (t80) REVERT: M 466 PHE cc_start: 0.6781 (t80) cc_final: 0.6056 (t80) REVERT: L 1 MET cc_start: 0.0438 (ptt) cc_final: 0.0094 (ptp) REVERT: L 74 ASN cc_start: 0.7959 (p0) cc_final: 0.7591 (m-40) REVERT: L 143 TRP cc_start: 0.4712 (m100) cc_final: 0.3577 (m100) REVERT: L 191 GLU cc_start: 0.8197 (pt0) cc_final: 0.7853 (tp30) REVERT: L 217 TRP cc_start: 0.5411 (t-100) cc_final: 0.4909 (t-100) REVERT: L 233 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.4027 (pp) REVERT: L 310 TYR cc_start: 0.7369 (m-10) cc_final: 0.7065 (m-10) REVERT: L 328 TRP cc_start: 0.1001 (p-90) cc_final: 0.0772 (p-90) REVERT: N 25 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6955 (tpt) REVERT: N 68 ARG cc_start: 0.6452 (tpp80) cc_final: 0.6196 (ttm110) REVERT: N 92 TYR cc_start: 0.4944 (t80) cc_final: 0.4593 (t80) REVERT: N 130 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6108 (mt) REVERT: N 159 TYR cc_start: 0.6738 (t80) cc_final: 0.6475 (t80) REVERT: N 223 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.3712 (m-10) REVERT: N 241 PHE cc_start: 0.8224 (t80) cc_final: 0.7992 (t80) REVERT: N 258 PHE cc_start: 0.7389 (t80) cc_final: 0.7001 (t80) REVERT: N 260 TYR cc_start: 0.5849 (m-80) cc_final: 0.5407 (m-80) REVERT: N 283 PHE cc_start: 0.5558 (m-80) cc_final: 0.5165 (m-80) REVERT: N 294 ILE cc_start: 0.6998 (tp) cc_final: 0.6481 (mp) REVERT: N 296 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7383 (ttm170) REVERT: N 321 MET cc_start: 0.7641 (ptp) cc_final: 0.7164 (ptt) REVERT: N 333 TYR cc_start: 0.5854 (t80) cc_final: 0.5120 (t80) REVERT: N 359 LEU cc_start: 0.7336 (tt) cc_final: 0.6780 (mp) REVERT: N 379 MET cc_start: 0.8175 (mmt) cc_final: 0.6970 (mmt) REVERT: N 392 PHE cc_start: 0.7241 (t80) cc_final: 0.6762 (t80) REVERT: N 425 TYR cc_start: 0.7347 (m-80) cc_final: 0.7007 (m-80) outliers start: 108 outliers final: 64 residues processed: 1029 average time/residue: 0.2180 time to fit residues: 364.6177 Evaluate side-chains 994 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 923 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 527 ASN Chi-restraints excluded: chain D residue 529 SER Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 878 THR Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 371 ILE 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: 7.9990 chunk 353 optimal weight: 30.0000 chunk 99 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 441 optimal weight: 20.0000 chunk 230 optimal weight: 0.9980 chunk 309 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 216 optimal weight: 0.4980 chunk 360 optimal weight: 10.0000 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 52 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 338 HIS ** 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 = 0.4734 r_free = 0.4734 target = 0.252707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.197616 restraints weight = 45888.529| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.10 r_work: 0.3592 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 36124 Z= 0.236 Angle : 0.820 45.756 49208 Z= 0.357 Chirality : 0.047 0.282 5554 Planarity : 0.005 0.054 6255 Dihedral : 5.650 173.668 4990 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.60 % Allowed : 17.60 % Favored : 78.80 % 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: -0.17 (0.12), residues: 4573 helix: 0.65 (0.10), residues: 2550 sheet: -0.14 (0.30), residues: 280 loop : -1.18 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 416 TYR 0.032 0.002 TYR G 709 PHE 0.035 0.002 PHE M 131 TRP 0.032 0.001 TRP F 25 HIS 0.015 0.002 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (36088) covalent geometry : angle 0.70609 / 0.36 (49115) hydrogen bonds : bond 0.04528 / 3.02 ( 1909) hydrogen bonds : angle 4.80986 / 3.34 ( 5502) metal coordination : bond 0.02072 / 1.21 ( 36) metal coordination : angle 9.63712 / 7.21 ( 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 1088 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 961 time to evaluate : 1.164 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 106 MET cc_start: 0.7880 (ppp) cc_final: 0.7497 (ppp) REVERT: B 202 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6926 (pt0) REVERT: B 215 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8139 (mtm180) REVERT: D 26 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7517 (mmt-90) REVERT: D 374 ARG cc_start: 0.7531 (ptp90) cc_final: 0.7166 (mtt90) REVERT: E 60 ASP cc_start: 0.8051 (m-30) cc_final: 0.7718 (m-30) REVERT: E 148 ASP cc_start: 0.8455 (t0) cc_final: 0.8021 (t0) REVERT: F 30 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7626 (mtm110) REVERT: F 100 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8081 (ptmm) REVERT: F 144 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8128 (mtt-85) REVERT: F 310 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8114 (mm-30) REVERT: G 537 ASN cc_start: 0.9117 (t0) cc_final: 0.8769 (t0) REVERT: G 551 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7360 (mp0) REVERT: G 562 ASP cc_start: 0.7061 (t0) cc_final: 0.6823 (t0) REVERT: G 886 MET cc_start: 0.9006 (mmm) cc_final: 0.8784 (mmt) REVERT: G 904 LYS cc_start: 0.7877 (pptt) cc_final: 0.7552 (pptt) REVERT: K 53 TRP cc_start: 0.8217 (m100) cc_final: 0.7680 (m100) REVERT: K 55 GLN cc_start: 0.3752 (pm20) cc_final: 0.3548 (pm20) REVERT: K 98 MET cc_start: 0.3160 (ptt) cc_final: 0.2852 (mtm) REVERT: J 64 MET cc_start: 0.5339 (mmm) cc_final: 0.5086 (tpt) REVERT: J 88 LEU cc_start: 0.6362 (mp) cc_final: 0.5945 (mm) REVERT: H 121 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4537 (tmm) REVERT: H 132 PHE cc_start: 0.6698 (m-80) cc_final: 0.6316 (m-80) REVERT: H 174 PHE cc_start: 0.3825 (m-10) cc_final: 0.3496 (m-80) REVERT: H 232 MET cc_start: 0.4699 (ptm) cc_final: 0.3604 (tpt) REVERT: H 278 PHE cc_start: 0.8608 (m-80) cc_final: 0.8398 (p90) REVERT: H 279 MET cc_start: 0.7928 (mmm) cc_final: 0.7614 (mmm) REVERT: H 280 MET cc_start: 0.7593 (mmp) cc_final: 0.7240 (mmp) REVERT: M 11 PHE cc_start: 0.7497 (m-80) cc_final: 0.6682 (m-80) REVERT: M 48 LEU cc_start: 0.8436 (tt) cc_final: 0.8005 (tp) REVERT: M 54 LEU cc_start: 0.4215 (pt) cc_final: 0.1787 (tt) REVERT: M 103 LEU cc_start: 0.8655 (mt) cc_final: 0.8312 (mt) REVERT: M 112 TYR cc_start: 0.6515 (p90) cc_final: 0.6210 (p90) REVERT: M 118 LEU cc_start: 0.9118 (tp) cc_final: 0.8324 (tt) REVERT: M 143 TRP cc_start: 0.6002 (t-100) cc_final: 0.5633 (t-100) REVERT: M 205 PHE cc_start: 0.5077 (m-10) cc_final: 0.4690 (m-10) REVERT: M 210 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6599 (mt) REVERT: M 222 LEU cc_start: 0.8288 (pp) cc_final: 0.7890 (mt) REVERT: M 318 THR cc_start: 0.6935 (p) cc_final: 0.6626 (p) REVERT: M 439 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4957 (mtt) REVERT: M 466 PHE cc_start: 0.6861 (t80) cc_final: 0.6607 (t80) REVERT: L 123 PHE cc_start: 0.9155 (t80) cc_final: 0.8860 (t80) REVERT: L 143 TRP cc_start: 0.4839 (m100) cc_final: 0.3744 (m100) REVERT: L 187 ILE cc_start: 0.7828 (tt) cc_final: 0.6923 (tt) REVERT: L 191 GLU cc_start: 0.8335 (pt0) cc_final: 0.7877 (tp30) REVERT: L 217 TRP cc_start: 0.5496 (t-100) cc_final: 0.5242 (t-100) REVERT: L 313 MET cc_start: 0.5421 (ptt) cc_final: 0.5174 (ptt) REVERT: L 569 MET cc_start: 0.4151 (tmm) cc_final: 0.2006 (ptt) REVERT: L 586 SER cc_start: 0.6914 (m) cc_final: 0.6651 (t) REVERT: N 25 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6806 (mmp) REVERT: N 67 MET cc_start: 0.5954 (ptm) cc_final: 0.5469 (pmm) REVERT: N 68 ARG cc_start: 0.6578 (tpp80) cc_final: 0.6361 (ttm110) REVERT: N 92 TYR cc_start: 0.4822 (t80) cc_final: 0.4575 (t80) REVERT: N 159 TYR cc_start: 0.6616 (t80) cc_final: 0.6329 (t80) REVERT: N 241 PHE cc_start: 0.8258 (t80) cc_final: 0.8037 (t80) REVERT: N 256 ARG cc_start: 0.6695 (mmm160) cc_final: 0.6471 (mmm160) REVERT: N 258 PHE cc_start: 0.7219 (t80) cc_final: 0.6890 (t80) REVERT: N 260 TYR cc_start: 0.5983 (m-80) cc_final: 0.5631 (m-80) REVERT: N 283 PHE cc_start: 0.5824 (m-80) cc_final: 0.5399 (m-80) REVERT: N 294 ILE cc_start: 0.7115 (tp) cc_final: 0.6621 (mp) REVERT: N 321 MET cc_start: 0.7592 (ptp) cc_final: 0.7106 (ptt) REVERT: N 323 MET cc_start: 0.4532 (ptt) cc_final: 0.3843 (ptt) REVERT: N 333 TYR cc_start: 0.5840 (t80) cc_final: 0.4899 (t80) REVERT: N 359 LEU cc_start: 0.7221 (tt) cc_final: 0.6779 (mp) REVERT: N 379 MET cc_start: 0.7930 (mmt) cc_final: 0.7339 (mmp) REVERT: N 392 PHE cc_start: 0.7213 (t80) cc_final: 0.6779 (t80) REVERT: N 397 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6639 (m-10) REVERT: N 425 TYR cc_start: 0.7222 (m-80) cc_final: 0.7018 (m-80) REVERT: N 434 LEU cc_start: 0.5107 (tp) cc_final: 0.4785 (mt) outliers start: 127 outliers final: 87 residues processed: 1019 average time/residue: 0.2164 time to fit residues: 359.8805 Evaluate side-chains 977 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 884 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 466 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 878 THR Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 595 VAL Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 281 ILE Chi-restraints excluded: chain N residue 305 HIS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 340 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 263 optimal weight: 30.0000 chunk 327 optimal weight: 40.0000 chunk 367 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 345 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 362 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 ASN D 397 ASN D 527 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 HIS G 259 HIS G 384 GLN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 ASN G 766 ASN G 826 GLN G 881 GLN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.244631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187276 restraints weight = 45611.009| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.20 r_work: 0.3441 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.253 36124 Z= 0.570 Angle : 1.134 65.846 49208 Z= 0.499 Chirality : 0.065 0.638 5554 Planarity : 0.007 0.112 6255 Dihedral : 6.388 174.275 4990 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.62 % Allowed : 18.96 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.96 (0.12), residues: 4573 helix: 0.18 (0.10), residues: 2527 sheet: -1.02 (0.29), residues: 285 loop : -1.70 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 45 TYR 0.049 0.003 TYR G 128 PHE 0.048 0.003 PHE M 131 TRP 0.076 0.003 TRP M 122 HIS 0.019 0.003 HIS D 514 Details of bonding type rmsd/Z covalent geometry : bond 0.01344 / 0.57 (36088) covalent geometry : angle 0.98107 / 0.50 (49115) hydrogen bonds : bond 0.05960 / 3.99 ( 1909) hydrogen bonds : angle 5.39918 / 3.76 ( 5502) metal coordination : bond 0.04600 / 2.51 ( 36) metal coordination : angle 13.10077 / 9.84 ( 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 1062 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 899 time to evaluate : 1.312 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 47 ASN cc_start: 0.8501 (m-40) cc_final: 0.7887 (p0) REVERT: B 122 TRP cc_start: 0.7870 (m-90) cc_final: 0.7581 (m-90) REVERT: B 200 GLU cc_start: 0.7233 (mp0) cc_final: 0.6894 (tt0) REVERT: D 108 MET cc_start: 0.8400 (mtp) cc_final: 0.8126 (mtp) REVERT: D 297 ASP cc_start: 0.7922 (m-30) cc_final: 0.7675 (t0) REVERT: D 353 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7486 (mtp85) REVERT: D 509 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: E 145 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9010 (mm) REVERT: E 148 ASP cc_start: 0.8922 (t0) cc_final: 0.8253 (t0) REVERT: E 164 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7317 (ttm110) REVERT: F 35 TYR cc_start: 0.8093 (m-80) cc_final: 0.7422 (m-80) REVERT: F 39 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7164 (mtm-85) REVERT: F 62 ARG cc_start: 0.8456 (mmt180) cc_final: 0.7717 (mmt90) REVERT: F 67 PHE cc_start: 0.8429 (m-80) cc_final: 0.8154 (m-10) REVERT: F 107 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: F 166 ASP cc_start: 0.8119 (t0) cc_final: 0.7418 (p0) REVERT: G 125 PHE cc_start: 0.8569 (t80) cc_final: 0.8324 (t80) REVERT: G 328 LEU cc_start: 0.8977 (tp) cc_final: 0.8691 (tt) REVERT: G 334 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7693 (pm20) REVERT: G 562 ASP cc_start: 0.7294 (t0) cc_final: 0.6708 (t0) REVERT: G 784 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (ttp-170) REVERT: G 904 LYS cc_start: 0.7847 (pptt) cc_final: 0.7503 (pptt) REVERT: I 107 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: K 31 MET cc_start: 0.7505 (mpp) cc_final: 0.7278 (mpp) REVERT: K 53 TRP cc_start: 0.8491 (m100) cc_final: 0.7830 (m100) REVERT: H 121 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4205 (tmm) REVERT: H 132 PHE cc_start: 0.6781 (m-80) cc_final: 0.6364 (m-80) REVERT: H 174 PHE cc_start: 0.4579 (m-10) cc_final: 0.4321 (m-80) REVERT: H 232 MET cc_start: 0.4819 (ptm) cc_final: 0.3540 (tpt) REVERT: H 280 MET cc_start: 0.7608 (mmp) cc_final: 0.7194 (mmp) REVERT: M 33 LEU cc_start: 0.9085 (mt) cc_final: 0.8650 (pp) REVERT: M 44 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (tp) REVERT: M 112 TYR cc_start: 0.6510 (p90) cc_final: 0.5887 (p90) REVERT: M 117 HIS cc_start: 0.8053 (p90) cc_final: 0.7356 (p90) REVERT: M 128 ILE cc_start: 0.5879 (mt) cc_final: 0.5588 (mm) REVERT: M 143 TRP cc_start: 0.5931 (t-100) cc_final: 0.5581 (t-100) REVERT: M 210 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6753 (tp) REVERT: M 248 HIS cc_start: 0.8527 (m90) cc_final: 0.8210 (m90) REVERT: M 286 PHE cc_start: 0.6389 (t80) cc_final: 0.6136 (t80) REVERT: M 371 MET cc_start: 0.4955 (ptt) cc_final: 0.2809 (mmt) REVERT: M 377 LEU cc_start: 0.8986 (mt) cc_final: 0.8772 (tt) REVERT: M 412 PHE cc_start: 0.8853 (m-80) cc_final: 0.8016 (m-80) REVERT: M 437 LEU cc_start: 0.6808 (pp) cc_final: 0.6081 (pp) REVERT: M 471 LEU cc_start: 0.8113 (mm) cc_final: 0.7884 (mm) REVERT: L 25 TRP cc_start: -0.1107 (m-10) cc_final: -0.1440 (m-10) REVERT: L 123 PHE cc_start: 0.9120 (t80) cc_final: 0.8745 (t80) REVERT: L 143 TRP cc_start: 0.5096 (m100) cc_final: 0.4031 (m100) REVERT: L 191 GLU cc_start: 0.8205 (pt0) cc_final: 0.7896 (tp30) REVERT: L 199 GLU cc_start: 0.7404 (mp0) cc_final: 0.7074 (pm20) REVERT: L 217 TRP cc_start: 0.5621 (t-100) cc_final: 0.5396 (t-100) REVERT: L 569 MET cc_start: 0.4486 (tmm) cc_final: 0.2186 (ptt) REVERT: N 25 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7335 (mmp) REVERT: N 108 LEU cc_start: 0.7047 (mt) cc_final: 0.6833 (mt) REVERT: N 159 TYR cc_start: 0.6927 (t80) cc_final: 0.6458 (t80) REVERT: N 162 LEU cc_start: 0.5176 (mt) cc_final: 0.4946 (mt) REVERT: N 216 PHE cc_start: 0.7550 (t80) cc_final: 0.7144 (t80) REVERT: N 223 PHE cc_start: 0.4698 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: N 258 PHE cc_start: 0.7276 (t80) cc_final: 0.6814 (t80) REVERT: N 260 TYR cc_start: 0.5849 (m-80) cc_final: 0.5378 (m-80) REVERT: N 294 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6331 (pt) REVERT: N 321 MET cc_start: 0.7746 (ptp) cc_final: 0.7390 (ptt) REVERT: N 323 MET cc_start: 0.4679 (ptt) cc_final: 0.4060 (ptt) REVERT: N 359 LEU cc_start: 0.7291 (tt) cc_final: 0.6675 (mt) REVERT: N 379 MET cc_start: 0.8008 (mmt) cc_final: 0.6707 (mmp) REVERT: N 392 PHE cc_start: 0.7454 (t80) cc_final: 0.7056 (t80) REVERT: N 393 ILE cc_start: 0.6924 (mp) cc_final: 0.6700 (mt) REVERT: N 397 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6730 (m-10) outliers start: 163 outliers final: 116 residues processed: 984 average time/residue: 0.2176 time to fit residues: 347.7733 Evaluate side-chains 992 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 864 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 466 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 679 LYS Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 784 ARG Chi-restraints excluded: chain G residue 878 THR Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 300 TYR Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 595 VAL Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 414 VAL 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: 3.9990 chunk 87 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 384 optimal weight: 50.0000 chunk 388 optimal weight: 30.0000 chunk 191 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 397 ASN F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 750 GLN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 HIS ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN N 37 ASN N 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.251528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196338 restraints weight = 45775.905| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.35 r_work: 0.3556 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 36124 Z= 0.174 Angle : 0.841 56.041 49208 Z= 0.353 Chirality : 0.045 0.363 5554 Planarity : 0.005 0.052 6255 Dihedral : 5.739 171.687 4990 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.54 % Allowed : 21.43 % Favored : 75.03 % 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: 0.65 (0.10), residues: 2544 sheet: -0.54 (0.30), residues: 281 loop : -1.42 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 87 TYR 0.029 0.002 TYR M 435 PHE 0.050 0.002 PHE M 131 TRP 0.049 0.001 TRP M 122 HIS 0.016 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (36088) covalent geometry : angle 0.70162 / 0.35 (49115) hydrogen bonds : bond 0.04369 / 2.91 ( 1909) hydrogen bonds : angle 4.83049 / 3.35 ( 5502) metal coordination : bond 0.01573 / 0.90 ( 36) metal coordination : angle 10.67863 / 8.14 ( 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 1042 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 917 time to evaluate : 1.372 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: B 45 MET cc_start: 0.6803 (mmm) cc_final: 0.6600 (mmt) REVERT: B 200 GLU cc_start: 0.7019 (mp0) cc_final: 0.6692 (tt0) REVERT: B 219 GLU cc_start: 0.6374 (mm-30) cc_final: 0.6104 (mm-30) REVERT: D 26 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7915 (mmm160) REVERT: D 107 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8686 (tp) REVERT: D 347 GLU cc_start: 0.8017 (pt0) cc_final: 0.7515 (pt0) REVERT: D 353 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7653 (mtp85) REVERT: E 78 GLN cc_start: 0.8468 (mm110) cc_final: 0.8247 (mm110) REVERT: E 145 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8830 (mm) REVERT: E 148 ASP cc_start: 0.8867 (t0) cc_final: 0.8359 (t0) REVERT: F 35 TYR cc_start: 0.7873 (m-80) cc_final: 0.7436 (m-80) REVERT: F 67 PHE cc_start: 0.8379 (m-80) cc_final: 0.8095 (m-10) REVERT: F 100 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (ptmm) REVERT: F 101 ASP cc_start: 0.7473 (m-30) cc_final: 0.7236 (m-30) REVERT: F 252 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8272 (t80) REVERT: G 562 ASP cc_start: 0.7263 (t0) cc_final: 0.6664 (t0) REVERT: G 639 TYR cc_start: 0.8541 (m-80) cc_final: 0.8149 (m-80) REVERT: G 804 GLN cc_start: 0.8396 (tp40) cc_final: 0.8184 (tp-100) REVERT: G 904 LYS cc_start: 0.7861 (pptt) cc_final: 0.7493 (pptt) REVERT: K 31 MET cc_start: 0.7210 (mpp) cc_final: 0.6669 (mpp) REVERT: K 36 GLU cc_start: 0.5833 (mm-30) cc_final: 0.5216 (mm-30) REVERT: K 53 TRP cc_start: 0.8269 (m100) cc_final: 0.7533 (m100) REVERT: K 98 MET cc_start: 0.3453 (ptt) cc_final: 0.2918 (mtm) REVERT: J 146 MET cc_start: 0.5788 (mtp) cc_final: 0.5520 (mtp) REVERT: H 121 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4233 (tmm) REVERT: H 132 PHE cc_start: 0.6724 (m-80) cc_final: 0.6296 (m-80) REVERT: H 232 MET cc_start: 0.4778 (ptm) cc_final: 0.3593 (tpt) REVERT: H 257 PHE cc_start: 0.5665 (t80) cc_final: 0.5127 (t80) REVERT: H 280 MET cc_start: 0.7570 (mmp) cc_final: 0.7154 (mmp) REVERT: M 112 TYR cc_start: 0.6364 (p90) cc_final: 0.5997 (p90) REVERT: M 117 HIS cc_start: 0.8270 (p90) cc_final: 0.7548 (p90) REVERT: M 128 ILE cc_start: 0.5560 (mt) cc_final: 0.5306 (mm) REVERT: M 143 TRP cc_start: 0.5979 (t-100) cc_final: 0.5652 (t-100) REVERT: M 248 HIS cc_start: 0.8267 (m90) cc_final: 0.8016 (m90) REVERT: M 286 PHE cc_start: 0.6503 (t80) cc_final: 0.6210 (t80) REVERT: M 412 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: M 445 PHE cc_start: 0.3367 (t80) cc_final: 0.2628 (t80) REVERT: M 466 PHE cc_start: 0.6096 (t80) cc_final: 0.5805 (t80) REVERT: M 471 LEU cc_start: 0.8038 (mm) cc_final: 0.7834 (mm) REVERT: L 1 MET cc_start: 0.2946 (OUTLIER) cc_final: 0.2673 (pmm) REVERT: L 123 PHE cc_start: 0.8986 (t80) cc_final: 0.8618 (t80) REVERT: L 143 TRP cc_start: 0.4898 (m100) cc_final: 0.3964 (m100) REVERT: L 569 MET cc_start: 0.4763 (tmm) cc_final: 0.2962 (ptt) REVERT: N 25 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7143 (mmm) REVERT: N 52 LEU cc_start: 0.3539 (mt) cc_final: 0.2489 (mt) REVERT: N 108 LEU cc_start: 0.6965 (mt) cc_final: 0.6677 (mm) REVERT: N 159 TYR cc_start: 0.6772 (t80) cc_final: 0.6429 (t80) REVERT: N 216 PHE cc_start: 0.7340 (t80) cc_final: 0.7059 (t80) REVERT: N 258 PHE cc_start: 0.7201 (t80) cc_final: 0.6889 (t80) REVERT: N 260 TYR cc_start: 0.5516 (m-80) cc_final: 0.5227 (m-80) REVERT: N 294 ILE cc_start: 0.6996 (tp) cc_final: 0.6747 (mp) REVERT: N 321 MET cc_start: 0.7586 (ptp) cc_final: 0.7175 (ptt) REVERT: N 333 TYR cc_start: 0.5701 (t80) cc_final: 0.4794 (t80) REVERT: N 359 LEU cc_start: 0.7506 (tt) cc_final: 0.6984 (mp) REVERT: N 362 TYR cc_start: 0.6152 (m-10) cc_final: 0.5326 (m-10) REVERT: N 379 MET cc_start: 0.7970 (mmt) cc_final: 0.6625 (mmp) REVERT: N 392 PHE cc_start: 0.7379 (t80) cc_final: 0.6909 (t80) REVERT: N 393 ILE cc_start: 0.6801 (mp) cc_final: 0.6553 (mt) REVERT: N 397 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: N 425 TYR cc_start: 0.6952 (m-80) cc_final: 0.6539 (m-80) outliers start: 125 outliers final: 78 residues processed: 982 average time/residue: 0.2177 time to fit residues: 347.5862 Evaluate side-chains 964 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 877 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 529 SER Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 396 PHE Chi-restraints excluded: chain N residue 397 TYR 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: 0.2980 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN D 224 HIS D 397 ASN D 527 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 750 GLN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 HIS ** 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 = 0.4730 r_free = 0.4730 target = 0.252268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.195862 restraints weight = 45901.515| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.30 r_work: 0.3553 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4506 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= 0.166 Angle : 0.826 47.371 49208 Z= 0.353 Chirality : 0.044 0.291 5554 Planarity : 0.005 0.050 6255 Dihedral : 5.595 172.425 4990 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.51 % Allowed : 22.73 % Favored : 73.75 % 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: -0.12 (0.12), residues: 4573 helix: 0.81 (0.10), residues: 2541 sheet: -0.52 (0.29), residues: 296 loop : -1.31 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 87 TYR 0.028 0.002 TYR M 435 PHE 0.054 0.002 PHE M 131 TRP 0.045 0.001 TRP L 217 HIS 0.018 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (36088) covalent geometry : angle 0.71140 / 0.35 (49115) hydrogen bonds : bond 0.04186 / 2.80 ( 1909) hydrogen bonds : angle 4.75635 / 3.29 ( 5502) metal coordination : bond 0.01388 / 0.79 ( 36) metal coordination : angle 9.69902 / 7.44 ( 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 1034 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 910 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: B 219 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6162 (mm-30) REVERT: D 26 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7371 (mmt-90) REVERT: D 144 THR cc_start: 0.7779 (m) cc_final: 0.7578 (p) REVERT: D 353 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7668 (mtt-85) REVERT: D 527 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7938 (t0) REVERT: E 144 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (ttm) REVERT: E 145 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8778 (mm) REVERT: E 148 ASP cc_start: 0.8722 (t0) cc_final: 0.8354 (t0) REVERT: E 154 THR cc_start: 0.7527 (p) cc_final: 0.7269 (t) REVERT: F 35 TYR cc_start: 0.7923 (m-80) cc_final: 0.7488 (m-80) REVERT: F 39 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6973 (mtm-85) REVERT: F 94 MET cc_start: 0.8688 (tpp) cc_final: 0.8319 (tpp) REVERT: F 252 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8301 (t80) REVERT: F 271 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7053 (tpp80) REVERT: F 275 GLU cc_start: 0.8087 (mp0) cc_final: 0.7522 (mp0) REVERT: G 334 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7579 (pm20) REVERT: G 562 ASP cc_start: 0.7145 (t0) cc_final: 0.6536 (t0) REVERT: G 639 TYR cc_start: 0.8524 (m-80) cc_final: 0.8156 (m-80) REVERT: G 804 GLN cc_start: 0.8400 (tp40) cc_final: 0.8109 (tp-100) REVERT: G 904 LYS cc_start: 0.7856 (pptt) cc_final: 0.7487 (pptt) REVERT: K 31 MET cc_start: 0.6994 (mpp) cc_final: 0.6519 (mpp) REVERT: K 36 GLU cc_start: 0.5745 (mm-30) cc_final: 0.5143 (mm-30) REVERT: K 53 TRP cc_start: 0.8331 (m100) cc_final: 0.7818 (m100) REVERT: K 98 MET cc_start: 0.3310 (ptt) cc_final: 0.2797 (mtm) REVERT: J 88 LEU cc_start: 0.6588 (mp) cc_final: 0.6158 (mm) REVERT: J 146 MET cc_start: 0.5790 (mtp) cc_final: 0.5496 (mtp) REVERT: H 121 MET cc_start: 0.4813 (OUTLIER) cc_final: 0.4203 (tmm) REVERT: H 232 MET cc_start: 0.4991 (ptm) cc_final: 0.3770 (tpt) REVERT: H 257 PHE cc_start: 0.5746 (t80) cc_final: 0.5227 (t80) REVERT: H 280 MET cc_start: 0.7357 (mmp) cc_final: 0.6971 (mmp) REVERT: H 281 MET cc_start: 0.8561 (tmm) cc_final: 0.7917 (ptp) REVERT: H 282 PHE cc_start: 0.8706 (m-10) cc_final: 0.8458 (m-10) REVERT: M 11 PHE cc_start: 0.7347 (m-80) cc_final: 0.6687 (m-80) REVERT: M 112 TYR cc_start: 0.6495 (p90) cc_final: 0.6058 (p90) REVERT: M 117 HIS cc_start: 0.8218 (p90) cc_final: 0.7421 (p90) REVERT: M 143 TRP cc_start: 0.5951 (t-100) cc_final: 0.5614 (t-100) REVERT: M 210 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6444 (tp) REVERT: M 224 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.4051 (mmt) REVERT: M 248 HIS cc_start: 0.8324 (m90) cc_final: 0.8090 (m90) REVERT: M 286 PHE cc_start: 0.6402 (t80) cc_final: 0.6136 (t80) REVERT: M 412 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: M 445 PHE cc_start: 0.3509 (t80) cc_final: 0.2766 (t80) REVERT: M 471 LEU cc_start: 0.8087 (mm) cc_final: 0.7881 (mm) REVERT: L 143 TRP cc_start: 0.5128 (m100) cc_final: 0.4377 (m100) REVERT: L 178 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: L 191 GLU cc_start: 0.7395 (tp30) cc_final: 0.7145 (tp30) REVERT: L 199 GLU cc_start: 0.7556 (pm20) cc_final: 0.7338 (pm20) REVERT: L 569 MET cc_start: 0.5057 (tmm) cc_final: 0.3236 (ptt) REVERT: N 25 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7125 (mmm) REVERT: N 52 LEU cc_start: 0.3314 (mt) cc_final: 0.2308 (mt) REVERT: N 92 TYR cc_start: 0.5301 (t80) cc_final: 0.4989 (t80) REVERT: N 108 LEU cc_start: 0.7018 (mt) cc_final: 0.6733 (mm) REVERT: N 159 TYR cc_start: 0.6793 (t80) cc_final: 0.6409 (t80) REVERT: N 203 LEU cc_start: 0.4800 (mt) cc_final: 0.4373 (pt) REVERT: N 216 PHE cc_start: 0.7433 (t80) cc_final: 0.7156 (t80) REVERT: N 258 PHE cc_start: 0.7574 (t80) cc_final: 0.7228 (t80) REVERT: N 260 TYR cc_start: 0.5623 (m-80) cc_final: 0.5236 (m-80) REVERT: N 294 ILE cc_start: 0.7049 (tp) cc_final: 0.6828 (mp) REVERT: N 321 MET cc_start: 0.7536 (ptp) cc_final: 0.7201 (ptt) REVERT: N 333 TYR cc_start: 0.5525 (t80) cc_final: 0.4784 (t80) REVERT: N 359 LEU cc_start: 0.7552 (tt) cc_final: 0.7114 (mp) REVERT: N 362 TYR cc_start: 0.6245 (m-10) cc_final: 0.5525 (m-10) REVERT: N 379 MET cc_start: 0.8014 (mmt) cc_final: 0.6705 (mmp) REVERT: N 392 PHE cc_start: 0.7305 (t80) cc_final: 0.6823 (t80) REVERT: N 393 ILE cc_start: 0.6769 (mp) cc_final: 0.6486 (mt) REVERT: N 397 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: N 425 TYR cc_start: 0.7092 (m-80) cc_final: 0.6602 (m-80) REVERT: N 482 MET cc_start: 0.3517 (ptp) cc_final: 0.3153 (ppp) outliers start: 124 outliers final: 95 residues processed: 967 average time/residue: 0.2029 time to fit residues: 321.2112 Evaluate side-chains 984 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 878 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 527 ASN Chi-restraints excluded: chain D residue 529 SER Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain L residue 117 PHE Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 366 PHE Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 ASN B 92 GLN B 167 GLN D 397 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 HIS ** 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 = 0.4724 r_free = 0.4724 target = 0.251674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196369 restraints weight = 45890.296| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.28 r_work: 0.3550 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4648 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= 0.188 Angle : 0.823 42.560 49208 Z= 0.357 Chirality : 0.045 0.234 5554 Planarity : 0.005 0.049 6255 Dihedral : 5.545 168.692 4990 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.60 % Allowed : 23.30 % Favored : 73.10 % 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: -0.07 (0.12), residues: 4573 helix: 0.85 (0.10), residues: 2529 sheet: -0.41 (0.30), residues: 296 loop : -1.27 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 145 TYR 0.028 0.002 TYR M 435 PHE 0.053 0.002 PHE M 131 TRP 0.037 0.001 TRP L 217 HIS 0.021 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (36088) covalent geometry : angle 0.71572 / 0.36 (49115) hydrogen bonds : bond 0.04273 / 2.86 ( 1909) hydrogen bonds : angle 4.76252 / 3.31 ( 5502) metal coordination : bond 0.01633 / 0.90 ( 36) metal coordination : angle 9.36733 / 7.19 ( 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 1019 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 892 time to evaluate : 1.260 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 45 MET cc_start: 0.7066 (mmt) cc_final: 0.6499 (mpp) REVERT: B 219 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5710 (mm-30) REVERT: D 26 ARG cc_start: 0.8078 (mmt180) cc_final: 0.7404 (mmt-90) REVERT: D 255 MET cc_start: 0.8434 (tpp) cc_final: 0.8068 (tpp) REVERT: D 353 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7786 (mtp85) REVERT: D 537 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8128 (mtmm) REVERT: E 144 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8524 (ttm) REVERT: E 145 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8823 (mm) REVERT: E 148 ASP cc_start: 0.8699 (t0) cc_final: 0.8335 (t0) REVERT: F 35 TYR cc_start: 0.7961 (m-80) cc_final: 0.7520 (m-80) REVERT: F 39 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: F 94 MET cc_start: 0.8713 (tpp) cc_final: 0.8367 (tpp) REVERT: F 252 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8265 (t80) REVERT: G 334 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7690 (pm20) REVERT: G 550 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: G 562 ASP cc_start: 0.7284 (t0) cc_final: 0.6847 (t0) REVERT: G 639 TYR cc_start: 0.8501 (m-80) cc_final: 0.8122 (m-80) REVERT: G 904 LYS cc_start: 0.7875 (pptt) cc_final: 0.7499 (pptt) REVERT: K 36 GLU cc_start: 0.5784 (mm-30) cc_final: 0.5168 (mm-30) REVERT: K 53 TRP cc_start: 0.8234 (m100) cc_final: 0.7715 (m100) REVERT: K 98 MET cc_start: 0.3661 (ptt) cc_final: 0.3106 (mtm) REVERT: J 88 LEU cc_start: 0.6452 (mp) cc_final: 0.6003 (mm) REVERT: J 146 MET cc_start: 0.5780 (mtp) cc_final: 0.5494 (mtp) REVERT: H 121 MET cc_start: 0.4927 (OUTLIER) cc_final: 0.4277 (tmm) REVERT: H 232 MET cc_start: 0.4716 (ptm) cc_final: 0.3621 (tpt) REVERT: H 280 MET cc_start: 0.7273 (mmp) cc_final: 0.6953 (mmp) REVERT: M 11 PHE cc_start: 0.7299 (m-80) cc_final: 0.6615 (m-80) REVERT: M 112 TYR cc_start: 0.6425 (p90) cc_final: 0.6037 (p90) REVERT: M 117 HIS cc_start: 0.8034 (p90) cc_final: 0.7760 (p-80) REVERT: M 209 GLU cc_start: 0.5457 (pm20) cc_final: 0.5251 (pm20) REVERT: M 224 MET cc_start: 0.4562 (OUTLIER) cc_final: 0.4093 (mmt) REVERT: M 248 HIS cc_start: 0.8325 (m90) cc_final: 0.8009 (m90) REVERT: M 374 MET cc_start: -0.2021 (mpp) cc_final: -0.2310 (mtm) REVERT: M 381 MET cc_start: 0.3560 (mmp) cc_final: 0.3253 (mmp) REVERT: M 412 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: M 445 PHE cc_start: 0.3782 (t80) cc_final: 0.3010 (t80) REVERT: L 123 PHE cc_start: 0.8942 (t80) cc_final: 0.8691 (t80) REVERT: L 152 LEU cc_start: 0.7849 (tp) cc_final: 0.7393 (pp) REVERT: L 178 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: L 217 TRP cc_start: 0.6404 (t-100) cc_final: 0.5950 (t-100) REVERT: L 229 LYS cc_start: 0.2022 (OUTLIER) cc_final: 0.1714 (ptmm) REVERT: L 569 MET cc_start: 0.5015 (tmm) cc_final: 0.3112 (ptt) REVERT: N 25 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7203 (mmm) REVERT: N 52 LEU cc_start: 0.3383 (mt) cc_final: 0.2358 (mt) REVERT: N 92 TYR cc_start: 0.5161 (t80) cc_final: 0.4842 (t80) REVERT: N 108 LEU cc_start: 0.6964 (mt) cc_final: 0.6665 (mm) REVERT: N 140 PHE cc_start: 0.4450 (m-80) cc_final: 0.4046 (m-80) REVERT: N 159 TYR cc_start: 0.6958 (t80) cc_final: 0.6685 (t80) REVERT: N 216 PHE cc_start: 0.7482 (t80) cc_final: 0.7143 (t80) REVERT: N 256 ARG cc_start: 0.6660 (mmm160) cc_final: 0.6442 (mmm160) REVERT: N 258 PHE cc_start: 0.7631 (t80) cc_final: 0.7294 (t80) REVERT: N 260 TYR cc_start: 0.5451 (m-80) cc_final: 0.5149 (m-80) REVERT: N 321 MET cc_start: 0.7609 (ptp) cc_final: 0.7281 (ptt) REVERT: N 359 LEU cc_start: 0.7571 (tt) cc_final: 0.7367 (mp) REVERT: N 362 TYR cc_start: 0.6940 (m-10) cc_final: 0.6384 (m-10) REVERT: N 379 MET cc_start: 0.7968 (mmt) cc_final: 0.6671 (mmp) REVERT: N 392 PHE cc_start: 0.7266 (t80) cc_final: 0.6771 (t80) REVERT: N 393 ILE cc_start: 0.6781 (mp) cc_final: 0.6504 (mt) REVERT: N 397 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: N 425 TYR cc_start: 0.7119 (m-80) cc_final: 0.6498 (m-80) REVERT: N 482 MET cc_start: 0.3640 (ptp) cc_final: 0.3369 (ppp) outliers start: 127 outliers final: 100 residues processed: 954 average time/residue: 0.2142 time to fit residues: 334.5547 Evaluate side-chains 983 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 872 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 550 GLU Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 721 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 175 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 229 LYS Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 366 PHE Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 359 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 388 optimal weight: 40.0000 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 420 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 397 ASN D 527 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.251163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.195855 restraints weight = 45642.008| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.32 r_work: 0.3535 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 36124 Z= 0.205 Angle : 0.841 40.310 49208 Z= 0.367 Chirality : 0.046 0.251 5554 Planarity : 0.005 0.048 6255 Dihedral : 5.545 168.492 4990 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 23.50 % Favored : 72.93 % 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: -0.09 (0.12), residues: 4573 helix: 0.82 (0.10), residues: 2536 sheet: -0.44 (0.30), residues: 300 loop : -1.26 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 145 TYR 0.049 0.002 TYR M 151 PHE 0.058 0.002 PHE M 131 TRP 0.030 0.001 TRP M 122 HIS 0.023 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (36088) covalent geometry : angle 0.73553 / 0.37 (49115) hydrogen bonds : bond 0.04338 / 2.91 ( 1909) hydrogen bonds : angle 4.78014 / 3.31 ( 5502) metal coordination : bond 0.01794 / 0.99 ( 36) metal coordination : angle 9.38573 / 7.19 ( 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 1034 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 908 time to evaluate : 1.306 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: B 45 MET cc_start: 0.6950 (mmt) cc_final: 0.6424 (mpp) REVERT: B 179 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: B 219 GLU cc_start: 0.6125 (mm-30) cc_final: 0.5860 (mm-30) REVERT: D 26 ARG cc_start: 0.8147 (mmt180) cc_final: 0.7403 (mmt-90) REVERT: D 353 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7736 (mtp85) REVERT: D 527 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (t0) REVERT: E 139 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8569 (mmmm) REVERT: E 144 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8640 (ttt) REVERT: E 145 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8820 (mm) REVERT: E 148 ASP cc_start: 0.8724 (t0) cc_final: 0.8326 (t0) REVERT: F 35 TYR cc_start: 0.7966 (m-80) cc_final: 0.7527 (m-80) REVERT: F 39 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6908 (mtm-85) REVERT: F 94 MET cc_start: 0.8739 (tpp) cc_final: 0.8338 (tpp) REVERT: F 178 TYR cc_start: 0.9095 (t80) cc_final: 0.8858 (t80) REVERT: F 252 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8272 (t80) REVERT: G 334 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7658 (pm20) REVERT: G 562 ASP cc_start: 0.7336 (t0) cc_final: 0.6870 (t0) REVERT: G 639 TYR cc_start: 0.8490 (m-80) cc_final: 0.8074 (m-80) REVERT: G 904 LYS cc_start: 0.7881 (pptt) cc_final: 0.7501 (pptt) REVERT: K 36 GLU cc_start: 0.5818 (mm-30) cc_final: 0.5195 (mm-30) REVERT: K 53 TRP cc_start: 0.8193 (m100) cc_final: 0.7693 (m100) REVERT: K 98 MET cc_start: 0.3709 (ptt) cc_final: 0.3103 (mtm) REVERT: J 88 LEU cc_start: 0.6490 (mp) cc_final: 0.6052 (mm) REVERT: J 146 MET cc_start: 0.5786 (mtp) cc_final: 0.5484 (mtp) REVERT: H 121 MET cc_start: 0.5037 (OUTLIER) cc_final: 0.4311 (tmm) REVERT: H 232 MET cc_start: 0.4727 (ptm) cc_final: 0.3632 (tpt) REVERT: H 280 MET cc_start: 0.7222 (mmp) cc_final: 0.6860 (mmp) REVERT: M 11 PHE cc_start: 0.7247 (m-80) cc_final: 0.6571 (m-80) REVERT: M 36 MET cc_start: 0.7935 (ptt) cc_final: 0.7709 (ptt) REVERT: M 112 TYR cc_start: 0.6442 (p90) cc_final: 0.6236 (p90) REVERT: M 117 HIS cc_start: 0.8115 (p90) cc_final: 0.7821 (p-80) REVERT: M 160 LYS cc_start: 0.5737 (mmtt) cc_final: 0.5509 (mmtt) REVERT: M 215 MET cc_start: 0.5178 (mmp) cc_final: 0.4774 (mmp) REVERT: M 248 HIS cc_start: 0.8218 (m90) cc_final: 0.7983 (m90) REVERT: M 382 LYS cc_start: -0.0286 (ptmm) cc_final: -0.3232 (tptp) REVERT: M 412 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: M 445 PHE cc_start: 0.3826 (t80) cc_final: 0.2941 (t80) REVERT: L 123 PHE cc_start: 0.8878 (t80) cc_final: 0.8618 (t80) REVERT: L 152 LEU cc_start: 0.7965 (tp) cc_final: 0.7512 (pp) REVERT: L 178 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: L 217 TRP cc_start: 0.6637 (t-100) cc_final: 0.6141 (t-100) REVERT: L 229 LYS cc_start: 0.1713 (OUTLIER) cc_final: 0.1407 (ptmm) REVERT: L 246 PRO cc_start: 0.8091 (Cg_exo) cc_final: 0.7599 (Cg_endo) REVERT: L 275 MET cc_start: 0.2365 (mtt) cc_final: 0.2054 (ptp) REVERT: L 569 MET cc_start: 0.5298 (tmm) cc_final: 0.3329 (ptt) REVERT: N 25 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7268 (mmm) REVERT: N 52 LEU cc_start: 0.3424 (mt) cc_final: 0.2347 (mt) REVERT: N 67 MET cc_start: 0.6395 (ppp) cc_final: 0.5941 (pmm) REVERT: N 108 LEU cc_start: 0.6972 (mt) cc_final: 0.6670 (mm) REVERT: N 140 PHE cc_start: 0.4353 (m-80) cc_final: 0.4045 (m-80) REVERT: N 159 TYR cc_start: 0.6975 (t80) cc_final: 0.6711 (t80) REVERT: N 216 PHE cc_start: 0.7578 (t80) cc_final: 0.7252 (t80) REVERT: N 241 PHE cc_start: 0.8344 (t80) cc_final: 0.7876 (m-80) REVERT: N 256 ARG cc_start: 0.6591 (mmm160) cc_final: 0.6275 (mmm160) REVERT: N 258 PHE cc_start: 0.7508 (t80) cc_final: 0.7193 (t80) REVERT: N 260 TYR cc_start: 0.5593 (m-80) cc_final: 0.5175 (m-80) REVERT: N 321 MET cc_start: 0.7516 (ptp) cc_final: 0.7221 (ptt) REVERT: N 359 LEU cc_start: 0.7648 (tt) cc_final: 0.7360 (mp) REVERT: N 379 MET cc_start: 0.7867 (mmt) cc_final: 0.6543 (mmp) REVERT: N 392 PHE cc_start: 0.7175 (t80) cc_final: 0.6696 (t80) REVERT: N 393 ILE cc_start: 0.6773 (mp) cc_final: 0.6511 (mt) REVERT: N 397 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6785 (m-10) REVERT: N 425 TYR cc_start: 0.6950 (m-80) cc_final: 0.6458 (m-80) outliers start: 126 outliers final: 101 residues processed: 971 average time/residue: 0.2186 time to fit residues: 345.9626 Evaluate side-chains 997 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 885 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 527 ASN Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 466 ASP Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 721 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 229 LYS Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 366 PHE Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 422 LEU 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: 0.8980 chunk 133 optimal weight: 0.3980 chunk 137 optimal weight: 0.0980 chunk 359 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 397 ASN D 514 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 881 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 HIS ** 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 = 0.4741 r_free = 0.4741 target = 0.253564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197977 restraints weight = 45797.687| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.22 r_work: 0.3592 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4831 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 : 0.818 34.298 49208 Z= 0.360 Chirality : 0.045 0.300 5554 Planarity : 0.005 0.057 6255 Dihedral : 5.434 169.215 4990 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.55 % Allowed : 24.91 % Favored : 72.53 % 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: 0.03 (0.12), residues: 4573 helix: 0.88 (0.10), residues: 2540 sheet: -0.19 (0.30), residues: 296 loop : -1.19 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 427 TYR 0.050 0.002 TYR M 151 PHE 0.061 0.002 PHE M 131 TRP 0.031 0.001 TRP M 122 HIS 0.024 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (36088) covalent geometry : angle 0.72592 / 0.36 (49115) hydrogen bonds : bond 0.04086 / 2.74 ( 1909) hydrogen bonds : angle 4.70445 / 3.26 ( 5502) metal coordination : bond 0.01155 / 0.66 ( 36) metal coordination : angle 8.68232 / 6.74 ( 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 1007 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 917 time to evaluate : 1.293 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 45 MET cc_start: 0.6986 (mmt) cc_final: 0.6377 (mpp) REVERT: B 179 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 219 GLU cc_start: 0.6004 (mm-30) cc_final: 0.5741 (mm-30) REVERT: D 26 ARG cc_start: 0.8115 (mmt180) cc_final: 0.7396 (mmt-90) REVERT: D 67 TYR cc_start: 0.8299 (m-80) cc_final: 0.7736 (m-80) REVERT: D 84 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7538 (mmm-85) REVERT: D 353 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7826 (mtp85) REVERT: E 110 GLU cc_start: 0.6391 (tm-30) cc_final: 0.6145 (tp30) REVERT: E 145 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8692 (mm) REVERT: E 148 ASP cc_start: 0.8643 (t0) cc_final: 0.8345 (t0) REVERT: F 1 MET cc_start: 0.5949 (ppp) cc_final: 0.5150 (ppp) REVERT: F 35 TYR cc_start: 0.7874 (m-80) cc_final: 0.7574 (m-80) REVERT: F 39 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.7036 (mtm-85) REVERT: F 94 MET cc_start: 0.8629 (tpp) cc_final: 0.8303 (tpp) REVERT: F 178 TYR cc_start: 0.9056 (t80) cc_final: 0.8824 (t80) REVERT: F 252 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8393 (t80) REVERT: F 310 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7249 (mm-30) REVERT: G 334 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7538 (pm20) REVERT: G 562 ASP cc_start: 0.7261 (t0) cc_final: 0.6904 (t0) REVERT: G 639 TYR cc_start: 0.8449 (m-80) cc_final: 0.8087 (m-80) REVERT: G 904 LYS cc_start: 0.7871 (pptt) cc_final: 0.7474 (pptt) REVERT: K 36 GLU cc_start: 0.5701 (mm-30) cc_final: 0.5086 (mm-30) REVERT: K 53 TRP cc_start: 0.8012 (m100) cc_final: 0.7516 (m100) REVERT: K 98 MET cc_start: 0.3808 (ptt) cc_final: 0.3286 (mtm) REVERT: J 88 LEU cc_start: 0.6320 (mp) cc_final: 0.5937 (mm) REVERT: J 146 MET cc_start: 0.5728 (mtp) cc_final: 0.5429 (mtp) REVERT: H 121 MET cc_start: 0.5042 (OUTLIER) cc_final: 0.4335 (tmm) REVERT: H 232 MET cc_start: 0.4898 (ptm) cc_final: 0.3760 (tpt) REVERT: H 280 MET cc_start: 0.7226 (mmp) cc_final: 0.6835 (mmp) REVERT: M 11 PHE cc_start: 0.7361 (m-80) cc_final: 0.6702 (m-80) REVERT: M 112 TYR cc_start: 0.6623 (p90) cc_final: 0.6243 (p90) REVERT: M 117 HIS cc_start: 0.8049 (p90) cc_final: 0.7819 (p-80) REVERT: M 224 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.4095 (mmt) REVERT: M 248 HIS cc_start: 0.8291 (m90) cc_final: 0.7922 (m90) REVERT: M 274 PHE cc_start: 0.8026 (m-80) cc_final: 0.6673 (m-80) REVERT: M 374 MET cc_start: -0.2767 (mpp) cc_final: -0.2996 (mtm) REVERT: M 381 MET cc_start: 0.3391 (mmp) cc_final: 0.3151 (mmp) REVERT: M 382 LYS cc_start: -0.0324 (ptmm) cc_final: -0.3249 (tptp) REVERT: M 412 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: M 445 PHE cc_start: 0.3805 (t80) cc_final: 0.3043 (t80) REVERT: L 123 PHE cc_start: 0.8893 (t80) cc_final: 0.8610 (t80) REVERT: L 152 LEU cc_start: 0.7953 (tp) cc_final: 0.7516 (pp) REVERT: L 178 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: L 199 GLU cc_start: 0.7449 (pm20) cc_final: 0.7197 (pm20) REVERT: L 214 MET cc_start: 0.6774 (mmm) cc_final: 0.5457 (ppp) REVERT: L 217 TRP cc_start: 0.6465 (t-100) cc_final: 0.6064 (t-100) REVERT: L 275 MET cc_start: 0.2578 (mtt) cc_final: 0.2301 (ptp) REVERT: L 569 MET cc_start: 0.5361 (tmm) cc_final: 0.3470 (ptt) REVERT: N 25 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7241 (mmm) REVERT: N 52 LEU cc_start: 0.3267 (mt) cc_final: 0.2098 (mt) REVERT: N 67 MET cc_start: 0.6338 (ppp) cc_final: 0.5873 (pmm) REVERT: N 108 LEU cc_start: 0.6874 (mt) cc_final: 0.6642 (mt) REVERT: N 140 PHE cc_start: 0.4034 (m-80) cc_final: 0.3663 (m-80) REVERT: N 159 TYR cc_start: 0.6939 (t80) cc_final: 0.6706 (t80) REVERT: N 216 PHE cc_start: 0.7547 (t80) cc_final: 0.7251 (t80) REVERT: N 256 ARG cc_start: 0.6576 (mmm160) cc_final: 0.6326 (mmm160) REVERT: N 258 PHE cc_start: 0.7567 (t80) cc_final: 0.7230 (t80) REVERT: N 260 TYR cc_start: 0.5473 (m-80) cc_final: 0.5045 (m-80) REVERT: N 321 MET cc_start: 0.7478 (ptp) cc_final: 0.7237 (ptt) REVERT: N 379 MET cc_start: 0.7867 (mmt) cc_final: 0.6527 (mmp) REVERT: N 392 PHE cc_start: 0.7146 (t80) cc_final: 0.6727 (t80) REVERT: N 393 ILE cc_start: 0.6845 (mp) cc_final: 0.6537 (mt) REVERT: N 397 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6835 (m-10) REVERT: N 423 TYR cc_start: 0.8181 (t80) cc_final: 0.7897 (t80) REVERT: N 425 TYR cc_start: 0.7011 (m-80) cc_final: 0.6493 (m-80) REVERT: N 482 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.3140 (ttm) outliers start: 90 outliers final: 73 residues processed: 958 average time/residue: 0.2151 time to fit residues: 334.9136 Evaluate side-chains 979 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 896 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 466 ASP Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 366 PHE Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 482 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 0.9980 chunk 280 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 0.2980 chunk 361 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 396 optimal weight: 40.0000 chunk 263 optimal weight: 8.9990 chunk 34 optimal weight: 0.0170 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 HIS D 397 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.253351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.197767 restraints weight = 45637.900| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 3.23 r_work: 0.3599 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.417 36124 Z= 0.221 Angle : 0.909 59.200 49208 Z= 0.436 Chirality : 0.046 0.652 5554 Planarity : 0.005 0.079 6255 Dihedral : 5.435 169.205 4990 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.78 % Allowed : 24.55 % Favored : 72.68 % Cbeta Deviations : 0.05 % 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: 0.03 (0.12), residues: 4573 helix: 0.88 (0.10), residues: 2540 sheet: -0.18 (0.30), residues: 296 loop : -1.19 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 30 TYR 0.103 0.002 TYR M 151 PHE 0.097 0.002 PHE M 175 TRP 0.025 0.001 TRP M 122 HIS 0.019 0.001 HIS M 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (36088) covalent geometry : angle 0.82813 / 0.44 (49115) hydrogen bonds : bond 0.04110 / 2.76 ( 1909) hydrogen bonds : angle 4.71955 / 3.27 ( 5502) metal coordination : bond 0.01146 / 0.64 ( 36) metal coordination : angle 8.67747 / 6.74 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12827.17 seconds wall clock time: 219 minutes 17.29 seconds (13157.29 seconds total)