Starting phenix.real_space_refine on Fri Mar 6 22:26:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nyr_12653/03_2026/7nyr_12653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nyr_12653/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nyr_12653/03_2026/7nyr_12653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nyr_12653/03_2026/7nyr_12653.map" model { file = "/net/cci-nas-00/data/ceres_data/7nyr_12653/03_2026/7nyr_12653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nyr_12653/03_2026/7nyr_12653.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35228 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1222 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4725 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3424 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 7044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7044 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "I" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 144} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 668 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1985 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TRP:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 21, 'TRANS': 482} Chain: "L" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4126 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 18, 'TRANS': 593} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'HIS:plan': 8, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 5, 'PHE:plan': 11, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 3, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 268 Chain: "N" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3543 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 810 SG CYS B 158 176.319 106.819 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: 7.26, 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: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 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: 0.81 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: 6.96 Time building geometry restraints manager: 3.75 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=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" CB CSX E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.34e+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=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.372 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 46235 1.70 - 3.40: 2355 3.40 - 5.10: 430 5.10 - 6.80: 80 6.80 - 8.50: 15 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 - 17.96: 19126 17.96 - 35.92: 1628 35.92 - 53.88: 281 53.88 - 71.85: 50 71.85 - 89.81: 20 Dihedral angle restraints: 21105 sinusoidal: 7917 harmonic: 13188 Sorted by residual: dihedral pdb=" CA TRP L 535 " pdb=" C TRP L 535 " pdb=" N TYR L 536 " pdb=" CA TYR L 536 " ideal model delta harmonic sigma weight residual 180.00 153.09 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 dihedral pdb=" CA THR L 237 " pdb=" C THR L 237 " pdb=" N TRP L 238 " pdb=" CA TRP L 238 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 21102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4318 0.054 - 0.108: 1043 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: 6256 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 6253 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: 2.510 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: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.950 Find NCS groups from input model: 0.260 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 : 0.006 0.122 36124 Z= 0.236 Angle : 1.249 52.596 49208 Z= 0.470 Chirality : 0.047 0.270 5554 Planarity : 0.007 0.087 6256 Dihedral : 13.949 89.808 12665 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 covalent geometry : bond 0.00537 (36088) covalent geometry : angle 0.87557 (49115) hydrogen bonds : bond 0.18192 ( 1909) hydrogen bonds : angle 6.87136 ( 5502) metal coordination : bond 0.03919 ( 36) metal coordination : angle 20.51001 ( 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 : 1.229 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: 0.7870 (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: 0.1071 (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: 0.4608 (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: 0.7235 (mt) REVERT: N 298 LEU cc_start: 0.4837 (mt) cc_final: 0.4226 (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: 0.4746 (tpp) outliers start: 29 outliers final: 7 residues processed: 1204 average time/residue: 0.2131 time to fit residues: 417.1874 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 : 1.233 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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** ** L 334 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 = 0.4784 r_free = 0.4784 target = 0.259502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.203682 restraints weight = 46850.958| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 3.24 r_work: 0.3618 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2400 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= 0.182 Angle : 0.843 45.950 49208 Z= 0.356 Chirality : 0.045 0.249 5554 Planarity : 0.005 0.068 6256 Dihedral : 5.254 87.551 5006 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.21 % Allowed : 12.53 % 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: 2526 sheet: -0.19 (0.30), residues: 281 loop : -1.17 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 30 TYR 0.032 0.002 TYR M 435 PHE 0.032 0.002 PHE H 132 TRP 0.038 0.002 TRP N 470 HIS 0.012 0.001 HIS L 338 Details of bonding type rmsd covalent geometry : bond 0.00416 (36088) covalent geometry : angle 0.68524 (49115) hydrogen bonds : bond 0.05134 ( 1909) hydrogen bonds : angle 5.00896 ( 5502) metal coordination : bond 0.01304 ( 36) metal coordination : angle 11.29775 ( 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 1098 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1020 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: 0.8092 (mmt180) cc_final: 0.7486 (mmt-90) REVERT: D 67 TYR cc_start: 0.8524 (m-80) cc_final: 0.8222 (m-80) REVERT: D 382 TRP cc_start: 0.7968 (t60) cc_final: 0.7699 (t60) REVERT: D 385 LYS cc_start: 0.7978 (pptt) cc_final: 0.7735 (pptt) REVERT: D 392 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7394 (pttm) REVERT: D 417 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: D 444 GLU cc_start: 0.8658 (pm20) cc_final: 0.8404 (pm20) REVERT: D 472 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7965 (mm-40) REVERT: E 112 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8497 (tttp) REVERT: E 136 ASN cc_start: 0.8479 (t0) cc_final: 0.7508 (t0) REVERT: E 139 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7514 (mtmm) REVERT: E 148 ASP cc_start: 0.8129 (t0) cc_final: 0.7745 (t0) REVERT: F 35 TYR cc_start: 0.7798 (m-80) cc_final: 0.7234 (m-80) REVERT: F 144 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8116 (mtt-85) REVERT: G 173 TYR cc_start: 0.8630 (m-80) cc_final: 0.8145 (m-80) REVERT: G 264 ASP cc_start: 0.7541 (m-30) cc_final: 0.7305 (m-30) REVERT: G 494 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7956 (mmmt) REVERT: G 537 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8887 (t0) REVERT: G 551 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7498 (mp0) REVERT: G 562 ASP cc_start: 0.7131 (t0) cc_final: 0.6654 (t0) REVERT: G 725 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7797 (ttt180) REVERT: G 886 MET cc_start: 0.8899 (mmm) cc_final: 0.8647 (mmt) REVERT: G 904 LYS cc_start: 0.7876 (pptt) cc_final: 0.7562 (pptt) REVERT: I 133 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7469 (mm-30) REVERT: K 31 MET cc_start: 0.7028 (mpp) cc_final: 0.6424 (mpp) REVERT: K 98 MET cc_start: 0.2558 (ptt) cc_final: 0.2269 (mtt) REVERT: J 64 MET cc_start: 0.4375 (mmm) cc_final: 0.4074 (tpt) REVERT: J 146 MET cc_start: 0.5747 (mtp) cc_final: 0.5400 (mtp) REVERT: H 121 MET cc_start: 0.4650 (OUTLIER) cc_final: 0.4142 (tmm) REVERT: H 132 PHE cc_start: 0.6568 (m-80) cc_final: 0.6314 (m-80) REVERT: H 232 MET cc_start: 0.5141 (ptm) cc_final: 0.4019 (tpt) REVERT: H 280 MET cc_start: 0.8035 (mmp) cc_final: 0.7741 (mmp) REVERT: H 282 PHE cc_start: 0.8754 (m-10) cc_final: 0.8498 (m-10) REVERT: M 48 LEU cc_start: 0.8642 (tt) cc_final: 0.7655 (mt) REVERT: M 103 LEU cc_start: 0.8590 (mt) cc_final: 0.8250 (mt) REVERT: M 128 ILE cc_start: 0.5642 (mt) cc_final: 0.4992 (mm) REVERT: M 131 PHE cc_start: 0.6709 (m-80) cc_final: 0.6503 (m-80) REVERT: M 274 PHE cc_start: 0.8140 (m-80) cc_final: 0.7253 (m-80) REVERT: M 411 LEU cc_start: 0.3913 (mt) cc_final: 0.3239 (tt) REVERT: M 466 PHE cc_start: 0.6626 (t80) cc_final: 0.6241 (t80) REVERT: M 470 LEU cc_start: 0.7876 (mt) cc_final: 0.7647 (mt) REVERT: L 68 MET cc_start: 0.8328 (mpp) cc_final: 0.7875 (mpp) REVERT: L 74 ASN cc_start: 0.8196 (p0) cc_final: 0.7674 (m-40) REVERT: L 168 MET cc_start: 0.3223 (mpp) cc_final: 0.1964 (ptm) REVERT: L 207 HIS cc_start: 0.6693 (t70) cc_final: 0.6245 (t70) REVERT: N 40 LEU cc_start: 0.9335 (mp) cc_final: 0.9089 (pp) REVERT: N 68 ARG cc_start: 0.6254 (tpp80) cc_final: 0.5864 (ttm110) REVERT: N 92 TYR cc_start: 0.4915 (t80) cc_final: 0.4489 (t80) REVERT: N 123 ASN cc_start: -0.1117 (t0) cc_final: -0.1646 (t0) REVERT: N 130 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6174 (mp) REVERT: N 159 TYR cc_start: 0.6675 (t80) cc_final: 0.6263 (t80) REVERT: N 162 LEU cc_start: 0.5671 (mt) cc_final: 0.5277 (mt) REVERT: N 203 LEU cc_start: 0.5148 (tp) cc_final: 0.4783 (pp) REVERT: N 256 ARG cc_start: 0.6578 (mmm160) cc_final: 0.6343 (mmm160) REVERT: N 258 PHE cc_start: 0.7272 (t80) cc_final: 0.6879 (t80) REVERT: N 341 PHE cc_start: 0.6352 (m-80) cc_final: 0.6114 (m-80) REVERT: N 376 MET cc_start: 0.8944 (tpp) cc_final: 0.8726 (tpp) REVERT: N 379 MET cc_start: 0.8100 (mmt) cc_final: 0.6794 (mmt) REVERT: N 380 MET cc_start: 0.7072 (tpp) cc_final: 0.6364 (tpp) REVERT: N 392 PHE cc_start: 0.7085 (t80) cc_final: 0.6718 (t80) REVERT: N 425 TYR cc_start: 0.7457 (m-80) cc_final: 0.6925 (m-80) outliers start: 78 outliers final: 46 residues processed: 1052 average time/residue: 0.2071 time to fit residues: 353.2441 Evaluate side-chains 992 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 940 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 112 LYS 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 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 313 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 374 MET 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 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 346 LEU 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: 8.9990 chunk 100 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 152 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 344 optimal weight: 0.0170 chunk 92 optimal weight: 0.6980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN 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 668 GLN G 760 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS N 293 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.256104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.200595 restraints weight = 46404.010| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.11 r_work: 0.3614 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36124 Z= 0.158 Angle : 0.780 43.713 49208 Z= 0.335 Chirality : 0.044 0.233 5554 Planarity : 0.005 0.088 6256 Dihedral : 4.946 89.643 4996 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.86 % Allowed : 15.96 % Favored : 81.18 % 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: -0.16 (0.12), residues: 4573 helix: 0.58 (0.10), residues: 2543 sheet: -0.10 (0.30), residues: 284 loop : -1.05 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 30 TYR 0.031 0.002 TYR M 435 PHE 0.039 0.002 PHE L 208 TRP 0.022 0.001 TRP F 25 HIS 0.013 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00358 (36088) covalent geometry : angle 0.65904 (49115) hydrogen bonds : bond 0.04435 ( 1909) hydrogen bonds : angle 4.76854 ( 5502) metal coordination : bond 0.01319 ( 36) metal coordination : angle 9.60637 ( 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 1082 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 981 time to evaluate : 1.249 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 55 TRP cc_start: 0.7138 (m-90) cc_final: 0.6782 (m-90) REVERT: D 26 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7485 (mmt-90) REVERT: D 136 GLU cc_start: 0.7722 (tt0) cc_final: 0.7421 (tt0) REVERT: D 374 ARG cc_start: 0.7484 (ptp90) cc_final: 0.7154 (ptp90) REVERT: D 385 LYS cc_start: 0.8119 (pptt) cc_final: 0.7663 (tmmt) REVERT: D 392 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7420 (pttm) REVERT: D 527 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7691 (t0) REVERT: E 60 ASP cc_start: 0.8080 (m-30) cc_final: 0.7673 (m-30) REVERT: E 148 ASP cc_start: 0.8139 (t0) cc_final: 0.7836 (t0) REVERT: F 35 TYR cc_start: 0.7943 (m-80) cc_final: 0.7432 (m-80) REVERT: F 144 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8141 (mtt-85) REVERT: G 173 TYR cc_start: 0.8617 (m-80) cc_final: 0.8342 (m-80) REVERT: G 494 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7960 (mmmt) REVERT: G 551 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7587 (mp0) REVERT: G 562 ASP cc_start: 0.7171 (t0) cc_final: 0.6758 (t0) REVERT: G 597 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7936 (tpp-160) REVERT: G 904 LYS cc_start: 0.7821 (pptt) cc_final: 0.7509 (pptt) REVERT: I 84 ASP cc_start: 0.7359 (t0) cc_final: 0.6970 (t0) REVERT: K 31 MET cc_start: 0.7155 (mpp) cc_final: 0.6856 (mpp) REVERT: K 53 TRP cc_start: 0.8345 (m100) cc_final: 0.7660 (m100) REVERT: K 98 MET cc_start: 0.2653 (ptt) cc_final: 0.2254 (ptp) REVERT: J 64 MET cc_start: 0.4662 (mmm) cc_final: 0.4364 (tpt) REVERT: J 146 MET cc_start: 0.5737 (mtp) cc_final: 0.5371 (mtp) REVERT: H 121 MET cc_start: 0.4803 (OUTLIER) cc_final: 0.4137 (tmm) REVERT: H 132 PHE cc_start: 0.6524 (m-80) cc_final: 0.6146 (m-80) REVERT: H 174 PHE cc_start: 0.3824 (m-10) cc_final: 0.3584 (m-80) REVERT: H 232 MET cc_start: 0.4975 (ptm) cc_final: 0.3848 (tpt) REVERT: H 280 MET cc_start: 0.7743 (mmp) cc_final: 0.7404 (mmp) REVERT: M 93 LEU cc_start: 0.8484 (tp) cc_final: 0.8282 (tp) REVERT: M 103 LEU cc_start: 0.8644 (mt) cc_final: 0.8294 (mt) REVERT: M 112 TYR cc_start: 0.6973 (p90) cc_final: 0.6508 (p90) REVERT: M 117 HIS cc_start: 0.8589 (p90) cc_final: 0.8287 (p90) REVERT: M 128 ILE cc_start: 0.5476 (mt) cc_final: 0.4970 (mt) REVERT: M 143 TRP cc_start: 0.6043 (t-100) cc_final: 0.5717 (t-100) REVERT: M 186 LEU cc_start: 0.7647 (tp) cc_final: 0.7386 (tp) REVERT: M 210 LEU cc_start: 0.6974 (mt) cc_final: 0.6192 (tp) REVERT: M 222 LEU cc_start: 0.8579 (pp) cc_final: 0.8247 (mp) REVERT: M 224 MET cc_start: 0.6453 (ttt) cc_final: 0.6096 (mtt) REVERT: M 274 PHE cc_start: 0.8126 (m-80) cc_final: 0.7611 (m-80) REVERT: M 336 LEU cc_start: 0.8486 (tp) cc_final: 0.7923 (mp) REVERT: M 408 PHE cc_start: 0.8724 (t80) cc_final: 0.8430 (t80) REVERT: M 439 MET cc_start: 0.6022 (ttt) cc_final: 0.5767 (mtt) REVERT: M 460 MET cc_start: 0.0512 (pmm) cc_final: 0.0159 (pmm) REVERT: M 466 PHE cc_start: 0.6681 (t80) cc_final: 0.6120 (t80) REVERT: L 1 MET cc_start: 0.0411 (ptt) cc_final: 0.0044 (ptp) REVERT: L 74 ASN cc_start: 0.8147 (p0) cc_final: 0.7703 (m-40) REVERT: L 143 TRP cc_start: 0.4947 (m100) cc_final: 0.3745 (m100) REVERT: L 152 LEU cc_start: 0.7956 (tp) cc_final: 0.7746 (pt) REVERT: L 191 GLU cc_start: 0.8497 (pt0) cc_final: 0.7968 (tp30) REVERT: L 310 TYR cc_start: 0.7476 (m-10) cc_final: 0.7133 (m-10) REVERT: L 328 TRP cc_start: 0.1420 (p-90) cc_final: 0.1103 (p-90) REVERT: N 25 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7187 (tpt) REVERT: N 68 ARG cc_start: 0.6372 (tpp80) cc_final: 0.6084 (ttm110) REVERT: N 92 TYR cc_start: 0.4924 (t80) cc_final: 0.4554 (t80) REVERT: N 130 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5983 (mt) REVERT: N 159 TYR cc_start: 0.6730 (t80) cc_final: 0.6416 (t80) REVERT: N 223 PHE cc_start: 0.4604 (OUTLIER) cc_final: 0.3673 (m-10) REVERT: N 258 PHE cc_start: 0.7483 (t80) cc_final: 0.7068 (t80) REVERT: N 260 TYR cc_start: 0.5761 (m-80) cc_final: 0.5420 (m-80) REVERT: N 296 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7409 (ttm170) REVERT: N 321 MET cc_start: 0.7717 (ptp) cc_final: 0.7224 (ptt) REVERT: N 359 LEU cc_start: 0.7314 (tt) cc_final: 0.6793 (mp) REVERT: N 379 MET cc_start: 0.8199 (mmt) cc_final: 0.6994 (mmt) REVERT: N 392 PHE cc_start: 0.7278 (t80) cc_final: 0.6799 (t80) REVERT: N 425 TYR cc_start: 0.7509 (m-80) cc_final: 0.7104 (m-80) outliers start: 101 outliers final: 57 residues processed: 1030 average time/residue: 0.2055 time to fit residues: 342.6275 Evaluate side-chains 989 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 926 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 322 PHE 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 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 F residue 225 VAL Chi-restraints excluded: chain F residue 319 SER 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 188 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 312 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 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 147 LEU 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 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 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 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: 10.0000 chunk 353 optimal weight: 50.0000 chunk 99 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 441 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 360 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 198 GLN D 97 HIS D 397 ASN F 22 GLN F 52 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN G 537 ASN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN K 40 ASN J 22 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.253372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.198614 restraints weight = 45954.263| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.23 r_work: 0.3593 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 36124 Z= 0.217 Angle : 0.808 44.868 49208 Z= 0.350 Chirality : 0.046 0.281 5554 Planarity : 0.005 0.054 6256 Dihedral : 4.938 86.873 4992 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.49 % Allowed : 17.23 % Favored : 79.28 % 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: -0.06 (0.12), residues: 4573 helix: 0.70 (0.10), residues: 2548 sheet: -0.12 (0.30), residues: 295 loop : -1.08 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 416 TYR 0.029 0.002 TYR M 435 PHE 0.033 0.002 PHE M 131 TRP 0.028 0.001 TRP F 25 HIS 0.014 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00510 (36088) covalent geometry : angle 0.69492 (49115) hydrogen bonds : bond 0.04436 ( 1909) hydrogen bonds : angle 4.77225 ( 5502) metal coordination : bond 0.01836 ( 36) metal coordination : angle 9.51913 ( 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 1101 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 978 time to evaluate : 1.216 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 106 MET cc_start: 0.7952 (ppp) cc_final: 0.7434 (ppp) REVERT: B 202 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6968 (pt0) REVERT: B 215 ARG cc_start: 0.8377 (mtm180) cc_final: 0.8175 (mtm180) REVERT: D 26 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7571 (mmt-90) REVERT: D 374 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7178 (mtt90) REVERT: E 60 ASP cc_start: 0.8012 (m-30) cc_final: 0.7678 (m-30) REVERT: E 148 ASP cc_start: 0.8455 (t0) cc_final: 0.8025 (t0) REVERT: F 30 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7623 (mtm110) REVERT: F 35 TYR cc_start: 0.8038 (m-80) cc_final: 0.7524 (m-80) REVERT: F 100 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8029 (ptmm) REVERT: F 135 GLU cc_start: 0.6761 (tp30) cc_final: 0.6223 (tp30) REVERT: F 144 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8104 (mtt-85) REVERT: G 551 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7350 (mp0) REVERT: G 904 LYS cc_start: 0.7877 (pptt) cc_final: 0.7607 (pptt) REVERT: G 905 GLU cc_start: 0.7251 (mp0) cc_final: 0.6990 (mp0) REVERT: K 31 MET cc_start: 0.7269 (mpp) cc_final: 0.7007 (mpp) REVERT: K 53 TRP cc_start: 0.8204 (m100) cc_final: 0.7664 (m100) REVERT: K 55 GLN cc_start: 0.3893 (pm20) cc_final: 0.3688 (pm20) REVERT: K 98 MET cc_start: 0.3066 (ptt) cc_final: 0.2772 (mtm) REVERT: J 64 MET cc_start: 0.5330 (mmm) cc_final: 0.5066 (tpt) REVERT: J 88 LEU cc_start: 0.6356 (mp) cc_final: 0.5941 (mm) REVERT: H 121 MET cc_start: 0.5329 (ttm) cc_final: 0.4539 (tmm) REVERT: H 132 PHE cc_start: 0.6636 (m-80) cc_final: 0.6258 (m-80) REVERT: H 232 MET cc_start: 0.4754 (ptm) cc_final: 0.3721 (tpt) REVERT: H 257 PHE cc_start: 0.5655 (t80) cc_final: 0.5032 (t80) REVERT: H 280 MET cc_start: 0.7581 (mmp) cc_final: 0.7228 (mmp) REVERT: M 11 PHE cc_start: 0.7462 (m-80) cc_final: 0.6930 (m-80) REVERT: M 48 LEU cc_start: 0.8427 (tt) cc_final: 0.7683 (tp) REVERT: M 54 LEU cc_start: 0.4158 (pt) cc_final: 0.1723 (tt) REVERT: M 103 LEU cc_start: 0.8651 (mt) cc_final: 0.8309 (mt) REVERT: M 112 TYR cc_start: 0.6820 (p90) cc_final: 0.6484 (p90) REVERT: M 117 HIS cc_start: 0.8179 (p90) cc_final: 0.7465 (p90) REVERT: M 143 TRP cc_start: 0.6053 (t-100) cc_final: 0.5692 (t-100) REVERT: M 194 PHE cc_start: 0.4603 (t80) cc_final: 0.2751 (m-80) REVERT: M 210 LEU cc_start: 0.7073 (mt) cc_final: 0.6470 (mt) REVERT: M 211 LEU cc_start: 0.7962 (tp) cc_final: 0.7603 (tt) REVERT: M 222 LEU cc_start: 0.8321 (pp) cc_final: 0.7848 (mt) REVERT: M 223 LEU cc_start: 0.8807 (mp) cc_final: 0.8193 (mt) REVERT: M 314 LEU cc_start: 0.4616 (tp) cc_final: 0.4082 (tt) REVERT: M 411 LEU cc_start: 0.4641 (tp) cc_final: 0.3471 (pp) REVERT: M 460 MET cc_start: 0.0278 (pmm) cc_final: 0.0028 (pmm) REVERT: M 462 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4445 (tp) REVERT: M 466 PHE cc_start: 0.6554 (t80) cc_final: 0.5963 (t80) REVERT: M 470 LEU cc_start: 0.8344 (mt) cc_final: 0.8084 (mt) REVERT: L 123 PHE cc_start: 0.9131 (t80) cc_final: 0.8816 (t80) REVERT: L 143 TRP cc_start: 0.4785 (m100) cc_final: 0.3712 (m100) REVERT: L 151 TYR cc_start: 0.3554 (t80) cc_final: 0.3221 (t80) REVERT: L 191 GLU cc_start: 0.8313 (pt0) cc_final: 0.7830 (tp30) REVERT: L 217 TRP cc_start: 0.5684 (t-100) cc_final: 0.5216 (t-100) REVERT: L 313 MET cc_start: 0.5251 (ptt) cc_final: 0.5010 (ptt) REVERT: L 569 MET cc_start: 0.4226 (tmm) cc_final: 0.1947 (ptt) REVERT: N 25 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6796 (mmp) REVERT: N 67 MET cc_start: 0.5951 (ptm) cc_final: 0.5471 (pmm) REVERT: N 68 ARG cc_start: 0.6551 (tpp80) cc_final: 0.6349 (ttm110) REVERT: N 92 TYR cc_start: 0.4835 (t80) cc_final: 0.4590 (t80) REVERT: N 159 TYR cc_start: 0.6618 (t80) cc_final: 0.6361 (t80) REVERT: N 203 LEU cc_start: 0.4960 (mt) cc_final: 0.4649 (pt) REVERT: N 223 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.3977 (m-10) REVERT: N 241 PHE cc_start: 0.8223 (t80) cc_final: 0.7996 (t80) REVERT: N 248 ILE cc_start: 0.6998 (mt) cc_final: 0.6750 (mp) REVERT: N 256 ARG cc_start: 0.6587 (mmm160) cc_final: 0.6322 (mmm160) REVERT: N 258 PHE cc_start: 0.7192 (t80) cc_final: 0.6851 (t80) REVERT: N 260 TYR cc_start: 0.5919 (m-80) cc_final: 0.5542 (m-80) REVERT: N 321 MET cc_start: 0.7573 (ptp) cc_final: 0.7078 (ptt) REVERT: N 323 MET cc_start: 0.4463 (ptt) cc_final: 0.3843 (ptt) REVERT: N 333 TYR cc_start: 0.5829 (t80) cc_final: 0.4910 (t80) REVERT: N 359 LEU cc_start: 0.7415 (tt) cc_final: 0.6957 (mp) REVERT: N 379 MET cc_start: 0.7919 (mmt) cc_final: 0.7308 (mmp) REVERT: N 392 PHE cc_start: 0.7200 (t80) cc_final: 0.6723 (t80) REVERT: N 393 ILE cc_start: 0.6705 (mp) cc_final: 0.6400 (mp) REVERT: N 397 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6691 (m-10) outliers start: 123 outliers final: 82 residues processed: 1035 average time/residue: 0.2037 time to fit residues: 342.7545 Evaluate side-chains 979 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 892 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 167 GLN 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 397 ASN 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 552 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 22 GLN 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 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 502 THR Chi-restraints excluded: chain G residue 573 ARG Chi-restraints excluded: chain G residue 593 VAL 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 J residue 37 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET 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 477 LEU Chi-restraints excluded: chain L residue 178 ASP 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 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 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 286 LEU Chi-restraints excluded: chain N residue 305 HIS 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: 7.9990 chunk 341 optimal weight: 9.9990 chunk 263 optimal weight: 40.0000 chunk 327 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 233 optimal weight: 0.5980 chunk 345 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 362 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN B 213 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 334 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 HIS G 259 HIS G 537 ASN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 766 ASN G 826 GLN ** J 24 ASN ** 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** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.245717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188562 restraints weight = 45567.925| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.21 r_work: 0.3446 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.239 36124 Z= 0.530 Angle : 1.071 61.209 49208 Z= 0.474 Chirality : 0.062 0.606 5554 Planarity : 0.007 0.099 6256 Dihedral : 5.644 80.397 4989 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.62 % Allowed : 18.51 % Favored : 76.87 % 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: -0.75 (0.12), residues: 4573 helix: 0.30 (0.10), residues: 2539 sheet: -0.85 (0.28), residues: 303 loop : -1.57 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 45 TYR 0.049 0.003 TYR G 128 PHE 0.049 0.003 PHE M 131 TRP 0.048 0.002 TRP F 25 HIS 0.018 0.002 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.01248 (36088) covalent geometry : angle 0.93140 (49115) hydrogen bonds : bond 0.05650 ( 1909) hydrogen bonds : angle 5.27494 ( 5502) metal coordination : bond 0.04394 ( 36) metal coordination : angle 12.18360 ( 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 1057 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 894 time to evaluate : 1.058 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: B 122 TRP cc_start: 0.7861 (m-90) cc_final: 0.7597 (m-90) REVERT: B 200 GLU cc_start: 0.7245 (mp0) cc_final: 0.6865 (tt0) REVERT: D 107 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8756 (tp) REVERT: D 108 MET cc_start: 0.8387 (mtp) cc_final: 0.8066 (mtp) REVERT: D 115 GLU cc_start: 0.8168 (tt0) cc_final: 0.7739 (tp30) REVERT: D 353 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7591 (mtp85) REVERT: D 374 ARG cc_start: 0.7612 (ptp90) cc_final: 0.7352 (mtt90) REVERT: E 90 ARG cc_start: 0.8546 (mtp85) cc_final: 0.8307 (mtp85) REVERT: E 145 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9043 (mm) REVERT: E 148 ASP cc_start: 0.8976 (t0) cc_final: 0.8296 (t0) REVERT: E 164 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7346 (ttm110) REVERT: F 30 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7670 (mtm110) REVERT: F 166 ASP cc_start: 0.8104 (t0) cc_final: 0.7356 (p0) REVERT: G 125 PHE cc_start: 0.8445 (t80) cc_final: 0.8193 (t80) REVERT: G 328 LEU cc_start: 0.8882 (tp) cc_final: 0.8652 (tt) REVERT: G 334 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7604 (pm20) REVERT: G 562 ASP cc_start: 0.7108 (t0) cc_final: 0.6712 (t0) REVERT: G 804 GLN cc_start: 0.8420 (tp40) cc_final: 0.8161 (tp-100) REVERT: G 904 LYS cc_start: 0.7874 (pptt) cc_final: 0.7537 (pptt) REVERT: K 36 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5353 (mm-30) REVERT: K 53 TRP cc_start: 0.8466 (m100) cc_final: 0.7793 (m100) REVERT: K 98 MET cc_start: 0.3368 (ptt) cc_final: 0.2946 (mtm) REVERT: H 121 MET cc_start: 0.5007 (ttm) cc_final: 0.4290 (tmm) REVERT: H 132 PHE cc_start: 0.6840 (m-80) cc_final: 0.6381 (m-80) REVERT: H 174 PHE cc_start: 0.4432 (m-10) cc_final: 0.4177 (m-80) REVERT: H 232 MET cc_start: 0.4813 (ptm) cc_final: 0.3532 (tpt) REVERT: H 265 LEU cc_start: 0.3158 (pt) cc_final: 0.2920 (pp) REVERT: H 278 PHE cc_start: 0.8430 (m-80) cc_final: 0.8228 (p90) REVERT: H 279 MET cc_start: 0.7976 (mmm) cc_final: 0.7611 (mmm) REVERT: H 280 MET cc_start: 0.7597 (mmp) cc_final: 0.7222 (mmp) REVERT: M 117 HIS cc_start: 0.8250 (p90) cc_final: 0.7349 (p90) REVERT: M 128 ILE cc_start: 0.5706 (mt) cc_final: 0.5383 (mm) REVERT: M 143 TRP cc_start: 0.6032 (t-100) cc_final: 0.5823 (t-100) REVERT: M 210 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6616 (tp) REVERT: M 224 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3866 (ttm) REVERT: M 248 HIS cc_start: 0.8536 (m90) cc_final: 0.8200 (m90) REVERT: M 274 PHE cc_start: 0.8073 (m-80) cc_final: 0.7310 (m-10) REVERT: M 371 MET cc_start: 0.4920 (ptt) cc_final: 0.4029 (ptt) REVERT: M 373 MET cc_start: -0.2004 (OUTLIER) cc_final: -0.2581 (pmm) REVERT: M 377 LEU cc_start: 0.9090 (mt) cc_final: 0.8882 (tt) REVERT: M 437 LEU cc_start: 0.6753 (pp) cc_final: 0.6058 (pp) REVERT: M 445 PHE cc_start: 0.3971 (t80) cc_final: 0.3417 (t80) REVERT: M 462 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4603 (tp) REVERT: M 466 PHE cc_start: 0.6565 (t80) cc_final: 0.6107 (t80) REVERT: L 123 PHE cc_start: 0.9101 (t80) cc_final: 0.8754 (t80) REVERT: L 143 TRP cc_start: 0.5079 (m100) cc_final: 0.4057 (m100) REVERT: L 191 GLU cc_start: 0.8220 (pt0) cc_final: 0.7959 (tp30) REVERT: L 217 TRP cc_start: 0.5785 (t-100) cc_final: 0.5408 (t-100) REVERT: L 313 MET cc_start: 0.5452 (ptt) cc_final: 0.4758 (ptt) REVERT: L 569 MET cc_start: 0.4418 (tmm) cc_final: 0.2219 (ptt) REVERT: N 25 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7191 (mmm) REVERT: N 108 LEU cc_start: 0.7005 (mt) cc_final: 0.6620 (mt) REVERT: N 123 ASN cc_start: -0.0564 (t0) cc_final: -0.0776 (t0) REVERT: N 159 TYR cc_start: 0.6885 (t80) cc_final: 0.6456 (t80) REVERT: N 216 PHE cc_start: 0.7547 (t80) cc_final: 0.7196 (t80) REVERT: N 248 ILE cc_start: 0.6837 (mt) cc_final: 0.6614 (mt) REVERT: N 258 PHE cc_start: 0.7382 (t80) cc_final: 0.6973 (t80) REVERT: N 260 TYR cc_start: 0.5845 (m-80) cc_final: 0.5437 (m-80) REVERT: N 321 MET cc_start: 0.7684 (ptp) cc_final: 0.7287 (ptt) REVERT: N 323 MET cc_start: 0.4612 (ptt) cc_final: 0.4023 (ptt) REVERT: N 333 TYR cc_start: 0.5881 (t80) cc_final: 0.4966 (t80) REVERT: N 359 LEU cc_start: 0.7518 (tt) cc_final: 0.6889 (mp) REVERT: N 379 MET cc_start: 0.8080 (mmt) cc_final: 0.6814 (mmp) REVERT: N 392 PHE cc_start: 0.7479 (t80) cc_final: 0.7066 (t80) REVERT: N 393 ILE cc_start: 0.6947 (mp) cc_final: 0.6681 (mt) REVERT: N 397 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6829 (m-10) REVERT: N 425 TYR cc_start: 0.7039 (m-80) cc_final: 0.6708 (m-80) outliers start: 163 outliers final: 118 residues processed: 981 average time/residue: 0.2091 time to fit residues: 331.8758 Evaluate side-chains 986 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 860 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 430 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 470 LEU 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 142 ASN 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 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 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 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 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 506 SER Chi-restraints excluded: chain G residue 520 LEU 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 G residue 679 LYS Chi-restraints excluded: chain G residue 802 ARG Chi-restraints excluded: chain G residue 833 SER 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 1 MET 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 33 ILE Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 VAL 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 120 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 233 LEU 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 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 346 LEU Chi-restraints excluded: chain N residue 349 SER 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: 4.9990 chunk 87 optimal weight: 0.9980 chunk 268 optimal weight: 20.0000 chunk 384 optimal weight: 50.0000 chunk 388 optimal weight: 30.0000 chunk 191 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN D 527 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** J 24 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 159 HIS ** 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.253196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197456 restraints weight = 45766.801| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.12 r_work: 0.3578 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36124 Z= 0.156 Angle : 0.816 51.246 49208 Z= 0.347 Chirality : 0.044 0.250 5554 Planarity : 0.005 0.050 6256 Dihedral : 4.914 75.046 4985 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.06 % Allowed : 21.57 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4573 helix: 0.69 (0.10), residues: 2553 sheet: -0.41 (0.30), residues: 295 loop : -1.28 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 87 TYR 0.034 0.002 TYR D 390 PHE 0.054 0.002 PHE M 131 TRP 0.031 0.001 TRP F 25 HIS 0.018 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00357 (36088) covalent geometry : angle 0.69222 (49115) hydrogen bonds : bond 0.04238 ( 1909) hydrogen bonds : angle 4.76477 ( 5502) metal coordination : bond 0.01409 ( 36) metal coordination : angle 9.96432 ( 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 1031 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 923 time to evaluate : 1.181 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: B 200 GLU cc_start: 0.7017 (mp0) cc_final: 0.6640 (tt0) REVERT: D 26 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7554 (mmt-90) REVERT: D 78 GLU cc_start: 0.8360 (tt0) cc_final: 0.7944 (tt0) REVERT: D 84 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.5945 (mmm-85) REVERT: D 108 MET cc_start: 0.8188 (mtp) cc_final: 0.7877 (mtp) REVERT: D 115 GLU cc_start: 0.8082 (tt0) cc_final: 0.7695 (tp30) REVERT: D 347 GLU cc_start: 0.7957 (pt0) cc_final: 0.7415 (pt0) REVERT: D 353 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7627 (mtp85) REVERT: D 374 ARG cc_start: 0.7608 (ptp90) cc_final: 0.7137 (mtt90) REVERT: E 19 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.7588 (mtp-110) REVERT: E 70 GLU cc_start: 0.8768 (tp30) cc_final: 0.8553 (tp30) REVERT: E 78 GLN cc_start: 0.8257 (mm110) cc_final: 0.7836 (mm110) REVERT: E 112 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8661 (ttmt) REVERT: E 126 PHE cc_start: 0.7657 (m-80) cc_final: 0.7436 (m-80) REVERT: E 145 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8850 (mm) REVERT: E 148 ASP cc_start: 0.8748 (t0) cc_final: 0.8311 (t0) REVERT: F 22 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: F 25 TRP cc_start: 0.7275 (m100) cc_final: 0.6918 (m100) REVERT: F 30 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7652 (mtm110) REVERT: F 35 TYR cc_start: 0.7953 (m-80) cc_final: 0.7630 (m-80) REVERT: F 118 ILE cc_start: 0.9160 (mt) cc_final: 0.8951 (mt) REVERT: F 252 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8337 (t80) REVERT: G 562 ASP cc_start: 0.7201 (t0) cc_final: 0.6639 (t0) REVERT: G 639 TYR cc_start: 0.8445 (m-80) cc_final: 0.8122 (m-80) REVERT: G 810 TRP cc_start: 0.8503 (m100) cc_final: 0.8180 (m100) REVERT: G 904 LYS cc_start: 0.7836 (pptt) cc_final: 0.7462 (pptt) REVERT: K 36 GLU cc_start: 0.5664 (mm-30) cc_final: 0.5144 (mm-30) REVERT: K 53 TRP cc_start: 0.8318 (m100) cc_final: 0.7577 (m100) REVERT: K 98 MET cc_start: 0.3206 (ptt) cc_final: 0.2818 (mtm) REVERT: J 88 LEU cc_start: 0.6609 (mp) cc_final: 0.6193 (mm) REVERT: J 146 MET cc_start: 0.5661 (mtp) cc_final: 0.5324 (mtp) REVERT: H 121 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4343 (tmm) REVERT: H 132 PHE cc_start: 0.6670 (m-80) cc_final: 0.6241 (m-80) REVERT: H 232 MET cc_start: 0.4954 (ptm) cc_final: 0.3694 (tpt) REVERT: H 257 PHE cc_start: 0.5600 (t80) cc_final: 0.5002 (t80) REVERT: H 280 MET cc_start: 0.7626 (mmp) cc_final: 0.7210 (mmp) REVERT: M 117 HIS cc_start: 0.7909 (p90) cc_final: 0.7010 (p90) REVERT: M 128 ILE cc_start: 0.5841 (mt) cc_final: 0.5548 (mm) REVERT: M 143 TRP cc_start: 0.6053 (t-100) cc_final: 0.5688 (t-100) REVERT: M 248 HIS cc_start: 0.8437 (m90) cc_final: 0.8062 (m90) REVERT: M 274 PHE cc_start: 0.8120 (m-80) cc_final: 0.7480 (m-10) REVERT: M 286 PHE cc_start: 0.6606 (t80) cc_final: 0.6346 (t80) REVERT: M 377 LEU cc_start: 0.8986 (mt) cc_final: 0.8725 (tt) REVERT: M 412 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: M 445 PHE cc_start: 0.3886 (t80) cc_final: 0.3378 (t80) REVERT: M 460 MET cc_start: 0.0016 (pmm) cc_final: -0.0387 (pmm) REVERT: M 462 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4782 (tp) REVERT: M 466 PHE cc_start: 0.6552 (t80) cc_final: 0.6109 (t80) REVERT: L 1 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3607 (pmm) REVERT: L 123 PHE cc_start: 0.9059 (t80) cc_final: 0.8703 (t80) REVERT: L 143 TRP cc_start: 0.5167 (m100) cc_final: 0.4064 (m100) REVERT: L 178 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: L 313 MET cc_start: 0.5524 (ptt) cc_final: 0.5072 (ptt) REVERT: L 569 MET cc_start: 0.4654 (tmm) cc_final: 0.2889 (ptt) REVERT: L 586 SER cc_start: 0.7177 (m) cc_final: 0.6958 (t) REVERT: N 25 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7191 (mmm) REVERT: N 68 ARG cc_start: 0.6853 (ttm110) cc_final: 0.6517 (ttp-110) REVERT: N 159 TYR cc_start: 0.6662 (t80) cc_final: 0.6343 (t80) REVERT: N 203 LEU cc_start: 0.4715 (mt) cc_final: 0.4278 (pt) REVERT: N 248 ILE cc_start: 0.6720 (mt) cc_final: 0.6482 (mt) REVERT: N 258 PHE cc_start: 0.7343 (t80) cc_final: 0.6989 (t80) REVERT: N 260 TYR cc_start: 0.5598 (m-80) cc_final: 0.5230 (m-80) REVERT: N 321 MET cc_start: 0.7579 (ptp) cc_final: 0.7185 (ptt) REVERT: N 333 TYR cc_start: 0.5643 (t80) cc_final: 0.4763 (t80) REVERT: N 359 LEU cc_start: 0.7839 (tt) cc_final: 0.7107 (mp) REVERT: N 362 TYR cc_start: 0.6865 (m-80) cc_final: 0.6182 (m-80) REVERT: N 379 MET cc_start: 0.8010 (mmt) cc_final: 0.6711 (mmp) REVERT: N 392 PHE cc_start: 0.7316 (t80) cc_final: 0.6830 (t80) REVERT: N 393 ILE cc_start: 0.6813 (mp) cc_final: 0.6584 (mp) REVERT: N 397 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: N 425 TYR cc_start: 0.6911 (m-80) cc_final: 0.6498 (m-80) REVERT: N 427 ARG cc_start: 0.6244 (mtp180) cc_final: 0.5550 (mtm110) outliers start: 108 outliers final: 75 residues processed: 974 average time/residue: 0.2023 time to fit residues: 321.1673 Evaluate side-chains 960 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 875 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 497 THR Chi-restraints excluded: chain D residue 529 SER Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 145 ILE 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 225 VAL Chi-restraints excluded: chain F residue 229 LEU 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 92 VAL 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 292 THR Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 535 SER 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 802 ARG 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 J residue 74 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 321 LEU Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 276 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 M residue 462 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 233 LEU 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 25 MET Chi-restraints excluded: chain N residue 74 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 286 LEU Chi-restraints excluded: chain N residue 366 PHE 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: 9.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 289 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 131 ASN D 397 ASN D 527 ASN F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** J 24 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 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.253909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198822 restraints weight = 46123.028| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 3.27 r_work: 0.3603 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 36124 Z= 0.181 Angle : 0.818 44.513 49208 Z= 0.353 Chirality : 0.045 0.368 5554 Planarity : 0.005 0.050 6256 Dihedral : 4.824 71.826 4985 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.57 % Allowed : 21.94 % Favored : 74.49 % 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: 0.74 (0.10), residues: 2545 sheet: -0.39 (0.30), residues: 302 loop : -1.20 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 87 TYR 0.036 0.002 TYR N 423 PHE 0.068 0.002 PHE L 97 TRP 0.046 0.001 TRP L 217 HIS 0.017 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00419 (36088) covalent geometry : angle 0.70561 (49115) hydrogen bonds : bond 0.04237 ( 1909) hydrogen bonds : angle 4.73936 ( 5502) metal coordination : bond 0.01675 ( 36) metal coordination : angle 9.56208 ( 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: 126 poor density : 908 time to evaluate : 1.111 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: B 45 MET cc_start: 0.7085 (mmt) cc_final: 0.6533 (mpp) REVERT: D 26 ARG cc_start: 0.8123 (mmt180) cc_final: 0.7563 (mmt-90) REVERT: D 115 GLU cc_start: 0.8124 (tt0) cc_final: 0.7787 (tp30) REVERT: D 347 GLU cc_start: 0.7988 (pt0) cc_final: 0.7434 (pt0) REVERT: D 353 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7640 (mtp85) REVERT: D 374 ARG cc_start: 0.7565 (ptp90) cc_final: 0.7179 (mtt90) REVERT: D 527 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7842 (t0) REVERT: E 110 GLU cc_start: 0.6275 (tm-30) cc_final: 0.6051 (tp30) REVERT: E 144 MET cc_start: 0.8913 (ttp) cc_final: 0.8700 (ttm) REVERT: E 145 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8899 (mm) REVERT: E 148 ASP cc_start: 0.8727 (t0) cc_final: 0.8415 (t0) REVERT: F 22 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: F 35 TYR cc_start: 0.7986 (m-80) cc_final: 0.7719 (m-80) REVERT: F 94 MET cc_start: 0.8731 (tpp) cc_final: 0.8371 (tpp) REVERT: F 100 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: F 178 TYR cc_start: 0.9088 (t80) cc_final: 0.8812 (t80) REVERT: F 252 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8273 (t80) REVERT: F 275 GLU cc_start: 0.8005 (mp0) cc_final: 0.7572 (mp0) REVERT: G 334 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7669 (pm20) REVERT: G 562 ASP cc_start: 0.7108 (t0) cc_final: 0.6582 (t0) REVERT: G 639 TYR cc_start: 0.8476 (m-80) cc_final: 0.8134 (m-80) REVERT: G 810 TRP cc_start: 0.8552 (m100) cc_final: 0.8226 (m100) REVERT: G 904 LYS cc_start: 0.7914 (pptt) cc_final: 0.7570 (pptt) REVERT: K 36 GLU cc_start: 0.5731 (mm-30) cc_final: 0.5134 (mm-30) REVERT: K 53 TRP cc_start: 0.7985 (m100) cc_final: 0.7528 (m100) REVERT: K 98 MET cc_start: 0.3159 (ptt) cc_final: 0.2764 (mtm) REVERT: J 88 LEU cc_start: 0.6276 (mp) cc_final: 0.5858 (mm) REVERT: J 146 MET cc_start: 0.5669 (mtp) cc_final: 0.5303 (mtp) REVERT: H 121 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4606 (tmm) REVERT: H 132 PHE cc_start: 0.6743 (m-80) cc_final: 0.6348 (m-80) REVERT: H 232 MET cc_start: 0.4952 (ptm) cc_final: 0.3724 (tpt) REVERT: H 279 MET cc_start: 0.7902 (mmm) cc_final: 0.7673 (mmm) REVERT: H 280 MET cc_start: 0.7576 (mmp) cc_final: 0.7199 (mmp) REVERT: H 281 MET cc_start: 0.8435 (tmm) cc_final: 0.7888 (ptp) REVERT: H 282 PHE cc_start: 0.8553 (m-80) cc_final: 0.8216 (m-10) REVERT: M 11 PHE cc_start: 0.7265 (m-80) cc_final: 0.6621 (m-80) REVERT: M 117 HIS cc_start: 0.7904 (p90) cc_final: 0.6934 (p-80) REVERT: M 128 ILE cc_start: 0.5631 (mt) cc_final: 0.5336 (mm) REVERT: M 143 TRP cc_start: 0.6048 (t-100) cc_final: 0.5694 (t-100) REVERT: M 274 PHE cc_start: 0.8063 (m-80) cc_final: 0.7251 (m-10) REVERT: M 286 PHE cc_start: 0.6579 (t80) cc_final: 0.6295 (t80) REVERT: M 381 MET cc_start: 0.3735 (mmp) cc_final: 0.3290 (mmp) REVERT: M 412 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: M 445 PHE cc_start: 0.3506 (t80) cc_final: 0.2734 (t80) REVERT: M 466 PHE cc_start: 0.6623 (t80) cc_final: 0.6086 (t80) REVERT: M 471 LEU cc_start: 0.8254 (mm) cc_final: 0.7916 (mm) REVERT: L 1 MET cc_start: 0.3542 (OUTLIER) cc_final: 0.3317 (pmm) REVERT: L 143 TRP cc_start: 0.4875 (m100) cc_final: 0.4312 (m100) REVERT: L 178 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: L 191 GLU cc_start: 0.7081 (tp30) cc_final: 0.6871 (tp30) REVERT: L 199 GLU cc_start: 0.7849 (pm20) cc_final: 0.7440 (pm20) REVERT: L 313 MET cc_start: 0.5459 (ptt) cc_final: 0.4981 (ptt) REVERT: L 569 MET cc_start: 0.5066 (tmm) cc_final: 0.3092 (ptt) REVERT: L 586 SER cc_start: 0.7102 (m) cc_final: 0.6889 (t) REVERT: N 25 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7076 (mmm) REVERT: N 52 LEU cc_start: 0.3492 (mt) cc_final: 0.2343 (mt) REVERT: N 68 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6566 (ttp-110) REVERT: N 92 TYR cc_start: 0.5321 (t80) cc_final: 0.5025 (t80) REVERT: N 108 LEU cc_start: 0.6795 (mt) cc_final: 0.6492 (mm) REVERT: N 159 TYR cc_start: 0.6695 (t80) cc_final: 0.6396 (t80) REVERT: N 216 PHE cc_start: 0.7579 (t80) cc_final: 0.7256 (t80) REVERT: N 248 ILE cc_start: 0.6693 (mt) cc_final: 0.6490 (mt) REVERT: N 258 PHE cc_start: 0.7190 (t80) cc_final: 0.6891 (t80) REVERT: N 260 TYR cc_start: 0.5737 (m-80) cc_final: 0.5399 (m-80) REVERT: N 321 MET cc_start: 0.7539 (ptp) cc_final: 0.7194 (ptt) REVERT: N 333 TYR cc_start: 0.5789 (t80) cc_final: 0.5004 (t80) REVERT: N 359 LEU cc_start: 0.7809 (tt) cc_final: 0.7227 (mp) REVERT: N 362 TYR cc_start: 0.6735 (m-80) cc_final: 0.6067 (m-80) REVERT: N 366 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: N 379 MET cc_start: 0.7915 (mmt) cc_final: 0.6664 (mmp) REVERT: N 392 PHE cc_start: 0.7210 (t80) cc_final: 0.6715 (t80) REVERT: N 393 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6536 (mp) REVERT: N 397 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: N 423 TYR cc_start: 0.7844 (t80) cc_final: 0.7585 (t80) REVERT: N 425 TYR cc_start: 0.6895 (m-80) cc_final: 0.6488 (m-80) REVERT: N 482 MET cc_start: 0.3707 (ptp) cc_final: 0.3402 (ppp) outliers start: 126 outliers final: 91 residues processed: 966 average time/residue: 0.2041 time to fit residues: 321.7264 Evaluate side-chains 989 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 885 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASN 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 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 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 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 E residue 109 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 22 GLN 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 G residue 9 LYS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 92 VAL 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 292 THR 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 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 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 90 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 74 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 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 210 LEU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 362 LEU 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 144 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 233 LEU 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 25 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 132 ILE 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 346 LEU Chi-restraints excluded: chain N residue 366 PHE Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 393 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: 0.7980 chunk 38 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 362 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN D 224 HIS D 397 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 899 HIS ** J 24 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 348 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.255319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.202453 restraints weight = 45909.954| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.36 r_work: 0.3615 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36124 Z= 0.157 Angle : 0.802 39.248 49208 Z= 0.348 Chirality : 0.044 0.311 5554 Planarity : 0.005 0.048 6256 Dihedral : 4.703 67.857 4985 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.34 % Allowed : 22.85 % Favored : 73.81 % 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: -0.05 (0.12), residues: 4573 helix: 0.80 (0.10), residues: 2541 sheet: -0.21 (0.30), residues: 289 loop : -1.18 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 87 TYR 0.051 0.002 TYR M 151 PHE 0.064 0.002 PHE H 278 TRP 0.041 0.001 TRP F 25 HIS 0.019 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00360 (36088) covalent geometry : angle 0.69980 (49115) hydrogen bonds : bond 0.04094 ( 1909) hydrogen bonds : angle 4.70298 ( 5502) metal coordination : bond 0.01331 ( 36) metal coordination : angle 9.04255 ( 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 1023 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 905 time to evaluate : 1.194 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: B 45 MET cc_start: 0.6838 (mmt) cc_final: 0.6353 (mpp) REVERT: B 59 PHE cc_start: 0.8219 (t80) cc_final: 0.7971 (t80) REVERT: D 26 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7505 (mmt-90) REVERT: D 115 GLU cc_start: 0.8154 (tt0) cc_final: 0.7772 (tp30) REVERT: D 353 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7815 (mtt-85) REVERT: E 78 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7828 (mm110) REVERT: E 144 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: E 145 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8831 (mm) REVERT: E 148 ASP cc_start: 0.8773 (t0) cc_final: 0.8430 (t0) REVERT: F 35 TYR cc_start: 0.7998 (m-80) cc_final: 0.7796 (m-80) REVERT: F 94 MET cc_start: 0.8647 (tpp) cc_final: 0.8302 (tpp) REVERT: F 135 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: F 193 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8744 (ttm110) REVERT: F 252 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8236 (t80) REVERT: F 275 GLU cc_start: 0.8004 (mp0) cc_final: 0.7522 (mp0) REVERT: G 334 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7624 (pm20) REVERT: G 560 ARG cc_start: 0.6628 (mpp80) cc_final: 0.6386 (mpp80) REVERT: G 562 ASP cc_start: 0.7085 (t0) cc_final: 0.6565 (t0) REVERT: G 639 TYR cc_start: 0.8476 (m-80) cc_final: 0.8126 (m-80) REVERT: G 904 LYS cc_start: 0.7879 (pptt) cc_final: 0.7517 (pptt) REVERT: K 36 GLU cc_start: 0.5671 (mm-30) cc_final: 0.5057 (mm-30) REVERT: K 53 TRP cc_start: 0.8057 (m100) cc_final: 0.7702 (m100) REVERT: K 55 GLN cc_start: 0.3711 (pm20) cc_final: 0.3494 (pm20) REVERT: K 98 MET cc_start: 0.3408 (ptt) cc_final: 0.3001 (mtm) REVERT: J 88 LEU cc_start: 0.6262 (mp) cc_final: 0.5812 (mm) REVERT: J 146 MET cc_start: 0.5555 (mtp) cc_final: 0.5193 (mtp) REVERT: H 121 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.4618 (tmm) REVERT: H 132 PHE cc_start: 0.6761 (m-80) cc_final: 0.6396 (m-80) REVERT: H 232 MET cc_start: 0.4866 (ptm) cc_final: 0.3750 (tpt) REVERT: H 279 MET cc_start: 0.7756 (mmm) cc_final: 0.7545 (mmm) REVERT: H 280 MET cc_start: 0.6898 (mmp) cc_final: 0.6565 (mmp) REVERT: H 281 MET cc_start: 0.8345 (tmm) cc_final: 0.7855 (ptp) REVERT: H 282 PHE cc_start: 0.8530 (m-80) cc_final: 0.8207 (m-10) REVERT: M 11 PHE cc_start: 0.7231 (m-80) cc_final: 0.6598 (m-80) REVERT: M 103 LEU cc_start: 0.8084 (tp) cc_final: 0.7877 (tt) REVERT: M 117 HIS cc_start: 0.7854 (p90) cc_final: 0.6866 (p-80) REVERT: M 128 ILE cc_start: 0.5636 (mt) cc_final: 0.5338 (mm) REVERT: M 143 TRP cc_start: 0.5965 (t-100) cc_final: 0.5568 (t-100) REVERT: M 205 PHE cc_start: 0.4458 (m-80) cc_final: 0.3939 (m-80) REVERT: M 381 MET cc_start: 0.3409 (mmp) cc_final: 0.2976 (mmp) REVERT: M 391 PHE cc_start: 0.1198 (m-10) cc_final: 0.0947 (m-10) REVERT: M 412 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: M 445 PHE cc_start: 0.3540 (t80) cc_final: 0.2595 (t80) REVERT: M 466 PHE cc_start: 0.6665 (t80) cc_final: 0.5751 (t80) REVERT: M 499 TRP cc_start: 0.6115 (t-100) cc_final: 0.5893 (t-100) REVERT: L 123 PHE cc_start: 0.8834 (t80) cc_final: 0.8538 (t80) REVERT: L 152 LEU cc_start: 0.7693 (tp) cc_final: 0.7299 (pp) REVERT: L 178 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6237 (m-30) REVERT: L 191 GLU cc_start: 0.7028 (tp30) cc_final: 0.6806 (tp30) REVERT: L 217 TRP cc_start: 0.6343 (t-100) cc_final: 0.5926 (t-100) REVERT: L 229 LYS cc_start: 0.1645 (ptmm) cc_final: 0.1344 (ptmm) REVERT: L 313 MET cc_start: 0.5263 (ptt) cc_final: 0.4892 (ptt) REVERT: L 569 MET cc_start: 0.5339 (tmm) cc_final: 0.3422 (ptt) REVERT: L 586 SER cc_start: 0.7053 (m) cc_final: 0.6781 (t) REVERT: L 587 GLU cc_start: 0.3449 (tm-30) cc_final: 0.3117 (tm-30) REVERT: N 25 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7055 (mmm) REVERT: N 52 LEU cc_start: 0.3515 (mt) cc_final: 0.2332 (mt) REVERT: N 68 ARG cc_start: 0.6927 (ttm110) cc_final: 0.6621 (ttp-110) REVERT: N 92 TYR cc_start: 0.5209 (t80) cc_final: 0.4895 (t80) REVERT: N 108 LEU cc_start: 0.6763 (mt) cc_final: 0.6459 (mm) REVERT: N 159 TYR cc_start: 0.6672 (t80) cc_final: 0.6423 (t80) REVERT: N 203 LEU cc_start: 0.3767 (mt) cc_final: 0.3297 (pt) REVERT: N 216 PHE cc_start: 0.7662 (t80) cc_final: 0.7321 (t80) REVERT: N 256 ARG cc_start: 0.6692 (mmm160) cc_final: 0.6357 (mmm160) REVERT: N 258 PHE cc_start: 0.7247 (t80) cc_final: 0.7005 (t80) REVERT: N 259 LEU cc_start: 0.6190 (tt) cc_final: 0.5862 (tt) REVERT: N 260 TYR cc_start: 0.5837 (m-80) cc_final: 0.5361 (m-80) REVERT: N 287 MET cc_start: 0.6932 (mpp) cc_final: 0.6118 (mpp) REVERT: N 321 MET cc_start: 0.7529 (ptp) cc_final: 0.7191 (ptt) REVERT: N 359 LEU cc_start: 0.7826 (tt) cc_final: 0.7261 (mp) REVERT: N 362 TYR cc_start: 0.6803 (m-80) cc_final: 0.6070 (m-80) REVERT: N 366 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: N 379 MET cc_start: 0.7881 (mmt) cc_final: 0.6611 (mmp) REVERT: N 392 PHE cc_start: 0.7090 (t80) cc_final: 0.6605 (t80) REVERT: N 393 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6420 (mt) REVERT: N 397 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: N 423 TYR cc_start: 0.7820 (t80) cc_final: 0.7591 (t80) REVERT: N 425 TYR cc_start: 0.6955 (m-80) cc_final: 0.6753 (m-80) REVERT: N 482 MET cc_start: 0.3731 (ptp) cc_final: 0.3369 (ppp) outliers start: 118 outliers final: 86 residues processed: 960 average time/residue: 0.2073 time to fit residues: 323.7938 Evaluate side-chains 975 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 878 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 497 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 25 TRP 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 135 GLU 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 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 321 SER 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 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 90 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 74 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 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 210 LEU 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 412 PHE Chi-restraints excluded: chain M residue 439 MET 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 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 606 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE 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 393 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: 9.9990 chunk 70 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 71 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 420 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 899 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 179 GLN ** M 335 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 100 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 = 0.4764 r_free = 0.4764 target = 0.255941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.201480 restraints weight = 45741.112| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.25 r_work: 0.3622 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36124 Z= 0.152 Angle : 0.800 34.685 49208 Z= 0.352 Chirality : 0.044 0.290 5554 Planarity : 0.005 0.051 6256 Dihedral : 4.630 63.377 4985 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.09 % Allowed : 23.10 % Favored : 73.81 % 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: 0.01 (0.12), residues: 4573 helix: 0.82 (0.10), residues: 2540 sheet: -0.06 (0.31), residues: 289 loop : -1.15 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 448 TYR 0.037 0.002 TYR D 390 PHE 0.056 0.002 PHE M 131 TRP 0.029 0.001 TRP L 217 HIS 0.022 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00346 (36088) covalent geometry : angle 0.70619 (49115) hydrogen bonds : bond 0.04043 ( 1909) hydrogen bonds : angle 4.69440 ( 5502) metal coordination : bond 0.01228 ( 36) metal coordination : angle 8.68814 ( 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 996 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 887 time to evaluate : 1.271 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: D 26 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7368 (mmt-90) REVERT: D 115 GLU cc_start: 0.8136 (tt0) cc_final: 0.7748 (tp30) REVERT: D 353 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7805 (mtt-85) REVERT: E 90 ARG cc_start: 0.8422 (mtp85) cc_final: 0.7971 (mtm110) REVERT: E 145 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8835 (mm) REVERT: E 148 ASP cc_start: 0.8757 (t0) cc_final: 0.8497 (t0) REVERT: F 94 MET cc_start: 0.8592 (tpp) cc_final: 0.8294 (tpp) REVERT: F 118 ILE cc_start: 0.9218 (mt) cc_final: 0.8970 (mt) REVERT: F 252 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8313 (t80) REVERT: F 310 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7672 (mm-30) REVERT: G 334 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7576 (pm20) REVERT: G 562 ASP cc_start: 0.7039 (t0) cc_final: 0.6544 (t0) REVERT: G 639 TYR cc_start: 0.8448 (m-80) cc_final: 0.8088 (m-80) REVERT: G 904 LYS cc_start: 0.7882 (pptt) cc_final: 0.7479 (pptt) REVERT: K 36 GLU cc_start: 0.5743 (mm-30) cc_final: 0.5236 (mm-30) REVERT: K 53 TRP cc_start: 0.8008 (m100) cc_final: 0.7583 (m100) REVERT: K 98 MET cc_start: 0.3470 (ptt) cc_final: 0.2996 (mtm) REVERT: J 88 LEU cc_start: 0.6180 (mp) cc_final: 0.5767 (mm) REVERT: J 146 MET cc_start: 0.5589 (mtp) cc_final: 0.5189 (mtp) REVERT: H 121 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4459 (tmm) REVERT: H 232 MET cc_start: 0.4856 (ptm) cc_final: 0.3732 (tpt) REVERT: H 257 PHE cc_start: 0.5458 (t80) cc_final: 0.4838 (t80) REVERT: H 280 MET cc_start: 0.6876 (mmp) cc_final: 0.6445 (mmp) REVERT: M 7 ILE cc_start: 0.6550 (mp) cc_final: 0.6335 (mp) REVERT: M 11 PHE cc_start: 0.7441 (m-80) cc_final: 0.6819 (m-80) REVERT: M 36 MET cc_start: 0.7798 (ttp) cc_final: 0.7478 (ptt) REVERT: M 93 LEU cc_start: 0.7755 (tt) cc_final: 0.7324 (mt) REVERT: M 117 HIS cc_start: 0.8068 (p90) cc_final: 0.7084 (p-80) REVERT: M 128 ILE cc_start: 0.5701 (mt) cc_final: 0.5386 (mm) REVERT: M 224 MET cc_start: 0.4250 (OUTLIER) cc_final: 0.3466 (mtt) REVERT: M 274 PHE cc_start: 0.8169 (m-80) cc_final: 0.7670 (m-80) REVERT: M 381 MET cc_start: 0.3565 (mmp) cc_final: 0.3145 (mmp) REVERT: M 412 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: M 462 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4513 (tp) REVERT: M 499 TRP cc_start: 0.6248 (t-100) cc_final: 0.6042 (t-100) REVERT: L 123 PHE cc_start: 0.8909 (t80) cc_final: 0.8560 (t80) REVERT: L 152 LEU cc_start: 0.7792 (tp) cc_final: 0.7422 (pp) REVERT: L 178 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6386 (m-30) REVERT: L 191 GLU cc_start: 0.7235 (tp30) cc_final: 0.7025 (tp30) REVERT: L 217 TRP cc_start: 0.6190 (t-100) cc_final: 0.5700 (t-100) REVERT: L 313 MET cc_start: 0.5300 (ptt) cc_final: 0.4937 (ptt) REVERT: L 569 MET cc_start: 0.5167 (tmm) cc_final: 0.3280 (ptt) REVERT: L 586 SER cc_start: 0.7237 (m) cc_final: 0.6886 (t) REVERT: L 587 GLU cc_start: 0.3605 (tm-30) cc_final: 0.3265 (tm-30) REVERT: N 25 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7060 (mmm) REVERT: N 52 LEU cc_start: 0.3340 (mt) cc_final: 0.2177 (mt) REVERT: N 68 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6521 (ttp-110) REVERT: N 108 LEU cc_start: 0.6722 (mt) cc_final: 0.6408 (mm) REVERT: N 159 TYR cc_start: 0.6784 (t80) cc_final: 0.6529 (t80) REVERT: N 203 LEU cc_start: 0.3780 (mt) cc_final: 0.3299 (pt) REVERT: N 216 PHE cc_start: 0.7661 (t80) cc_final: 0.7348 (t80) REVERT: N 258 PHE cc_start: 0.7452 (t80) cc_final: 0.7162 (t80) REVERT: N 259 LEU cc_start: 0.6055 (tt) cc_final: 0.5768 (tt) REVERT: N 260 TYR cc_start: 0.5630 (m-80) cc_final: 0.5183 (m-80) REVERT: N 321 MET cc_start: 0.7549 (ptp) cc_final: 0.7218 (ptt) REVERT: N 359 LEU cc_start: 0.7781 (tt) cc_final: 0.7377 (mp) REVERT: N 366 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: N 379 MET cc_start: 0.7942 (mmt) cc_final: 0.6661 (mmp) REVERT: N 392 PHE cc_start: 0.7099 (t80) cc_final: 0.6698 (t80) REVERT: N 393 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6419 (mt) REVERT: N 397 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6834 (m-10) REVERT: N 423 TYR cc_start: 0.8210 (t80) cc_final: 0.7948 (t80) REVERT: N 425 TYR cc_start: 0.7079 (m-80) cc_final: 0.6848 (m-80) outliers start: 109 outliers final: 89 residues processed: 938 average time/residue: 0.2026 time to fit residues: 310.1133 Evaluate side-chains 964 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 864 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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 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 497 THR Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 145 ILE 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 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 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 293 LEU 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 537 ASN 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 90 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 74 LEU 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 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 210 LEU Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 451 GLN Chi-restraints excluded: chain M residue 462 LEU 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 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 25 MET Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 229 ASP 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 393 ILE Chi-restraints excluded: chain N residue 397 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 34 optimal weight: 3.9990 chunk 443 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 359 optimal weight: 6.9990 chunk 201 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 348 HIS ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.254751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.199968 restraints weight = 45580.430| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 3.27 r_work: 0.3594 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 36124 Z= 0.180 Angle : 0.828 33.628 49208 Z= 0.366 Chirality : 0.046 0.250 5554 Planarity : 0.005 0.082 6256 Dihedral : 4.673 60.452 4985 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.03 % Allowed : 23.38 % Favored : 73.58 % 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: -0.01 (0.12), residues: 4573 helix: 0.82 (0.10), residues: 2538 sheet: -0.12 (0.31), residues: 295 loop : -1.16 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 448 TYR 0.038 0.002 TYR D 390 PHE 0.055 0.002 PHE M 131 TRP 0.031 0.001 TRP L 217 HIS 0.013 0.001 HIS M 348 Details of bonding type rmsd covalent geometry : bond 0.00419 (36088) covalent geometry : angle 0.73591 (49115) hydrogen bonds : bond 0.04157 ( 1909) hydrogen bonds : angle 4.71398 ( 5502) metal coordination : bond 0.01576 ( 36) metal coordination : angle 8.77249 ( 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 982 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 875 time to evaluate : 1.109 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: B 179 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: D 26 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7350 (mmt-90) REVERT: D 115 GLU cc_start: 0.8161 (tt0) cc_final: 0.7742 (tp30) REVERT: D 353 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7863 (mtp85) REVERT: E 145 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8848 (mm) REVERT: E 148 ASP cc_start: 0.8686 (t0) cc_final: 0.8390 (t0) REVERT: E 164 ARG cc_start: 0.7534 (ptp-170) cc_final: 0.7075 (ptp-170) REVERT: F 94 MET cc_start: 0.8630 (tpp) cc_final: 0.8300 (tpp) REVERT: F 100 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8180 (ptmm) REVERT: F 135 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6361 (tp30) REVERT: F 252 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8323 (t80) REVERT: F 310 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7729 (mm-30) REVERT: G 334 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7544 (pm20) REVERT: G 562 ASP cc_start: 0.7101 (t0) cc_final: 0.6569 (t0) REVERT: G 639 TYR cc_start: 0.8489 (m-80) cc_final: 0.8085 (m-80) REVERT: G 888 MET cc_start: 0.7284 (mmt) cc_final: 0.6770 (mmm) REVERT: G 904 LYS cc_start: 0.7894 (pptt) cc_final: 0.7482 (pptt) REVERT: K 36 GLU cc_start: 0.5656 (mm-30) cc_final: 0.5171 (mm-30) REVERT: K 98 MET cc_start: 0.3509 (ptt) cc_final: 0.3021 (mtm) REVERT: J 88 LEU cc_start: 0.6154 (mp) cc_final: 0.5739 (mm) REVERT: J 146 MET cc_start: 0.5606 (mtp) cc_final: 0.5254 (mtp) REVERT: H 121 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4501 (tmm) REVERT: H 232 MET cc_start: 0.4877 (ptm) cc_final: 0.3742 (tpt) REVERT: H 280 MET cc_start: 0.6835 (mmp) cc_final: 0.6389 (mmp) REVERT: M 11 PHE cc_start: 0.7487 (m-80) cc_final: 0.6852 (m-80) REVERT: M 93 LEU cc_start: 0.7780 (tt) cc_final: 0.7271 (mt) REVERT: M 117 HIS cc_start: 0.8209 (p90) cc_final: 0.7338 (p-80) REVERT: M 128 ILE cc_start: 0.5656 (mt) cc_final: 0.5361 (mm) REVERT: M 205 PHE cc_start: 0.4466 (m-80) cc_final: 0.2486 (m-80) REVERT: M 224 MET cc_start: 0.4405 (OUTLIER) cc_final: 0.3613 (mtt) REVERT: M 381 MET cc_start: 0.3722 (mmp) cc_final: 0.3295 (mmp) REVERT: M 412 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: M 445 PHE cc_start: 0.4269 (t80) cc_final: 0.2985 (t80) REVERT: M 466 PHE cc_start: 0.5998 (t80) cc_final: 0.5623 (t80) REVERT: L 123 PHE cc_start: 0.8952 (t80) cc_final: 0.8594 (t80) REVERT: L 152 LEU cc_start: 0.7820 (tp) cc_final: 0.7456 (pp) REVERT: L 178 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6488 (m-30) REVERT: L 191 GLU cc_start: 0.7292 (tp30) cc_final: 0.7082 (tp30) REVERT: L 199 GLU cc_start: 0.7619 (pm20) cc_final: 0.7258 (pm20) REVERT: L 217 TRP cc_start: 0.6182 (t-100) cc_final: 0.5721 (t-100) REVERT: L 313 MET cc_start: 0.5072 (ptt) cc_final: 0.4435 (ptt) REVERT: L 569 MET cc_start: 0.5240 (tmm) cc_final: 0.3367 (ptt) REVERT: L 586 SER cc_start: 0.7217 (m) cc_final: 0.6858 (t) REVERT: L 587 GLU cc_start: 0.3670 (tm-30) cc_final: 0.3322 (tm-30) REVERT: N 25 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: N 52 LEU cc_start: 0.3244 (mt) cc_final: 0.2137 (mt) REVERT: N 68 ARG cc_start: 0.6652 (ttm110) cc_final: 0.6354 (ttp-110) REVERT: N 159 TYR cc_start: 0.6914 (t80) cc_final: 0.6637 (t80) REVERT: N 203 LEU cc_start: 0.3779 (mt) cc_final: 0.3302 (pt) REVERT: N 216 PHE cc_start: 0.7703 (t80) cc_final: 0.7385 (t80) REVERT: N 256 ARG cc_start: 0.6563 (mmm160) cc_final: 0.6276 (mmm160) REVERT: N 258 PHE cc_start: 0.7547 (t80) cc_final: 0.7227 (t80) REVERT: N 260 TYR cc_start: 0.5615 (m-80) cc_final: 0.5147 (m-80) REVERT: N 321 MET cc_start: 0.7454 (ptp) cc_final: 0.7203 (ptt) REVERT: N 333 TYR cc_start: 0.5600 (t80) cc_final: 0.5162 (t80) REVERT: N 359 LEU cc_start: 0.7861 (tt) cc_final: 0.7310 (mp) REVERT: N 362 TYR cc_start: 0.6815 (m-10) cc_final: 0.6382 (m-80) REVERT: N 366 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: N 379 MET cc_start: 0.7872 (mmt) cc_final: 0.6569 (mmp) REVERT: N 392 PHE cc_start: 0.7142 (t80) cc_final: 0.6764 (t80) REVERT: N 393 ILE cc_start: 0.6804 (mp) cc_final: 0.6467 (mt) REVERT: N 397 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: N 423 TYR cc_start: 0.8282 (t80) cc_final: 0.8076 (t80) REVERT: N 482 MET cc_start: 0.3382 (ptm) cc_final: 0.3161 (ttm) outliers start: 107 outliers final: 88 residues processed: 930 average time/residue: 0.2049 time to fit residues: 310.7717 Evaluate side-chains 964 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 864 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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 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 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 E residue 109 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 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 135 GLU 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 G residue 30 ILE 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 293 LEU 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 466 ASP 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 K residue 95 VAL Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 74 LEU 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 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 223 LEU Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 412 PHE Chi-restraints excluded: chain M residue 439 MET 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 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 25 MET Chi-restraints excluded: chain N residue 132 ILE Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 229 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 0.9980 chunk 280 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 361 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 210 optimal weight: 0.0670 chunk 396 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS ** 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 = 0.4763 r_free = 0.4763 target = 0.255870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201596 restraints weight = 45484.809| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 3.28 r_work: 0.3625 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36124 Z= 0.157 Angle : 0.815 31.692 49208 Z= 0.362 Chirality : 0.045 0.289 5554 Planarity : 0.005 0.080 6256 Dihedral : 4.603 58.493 4985 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 23.92 % Favored : 72.99 % 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: 0.86 (0.10), residues: 2545 sheet: 0.04 (0.31), residues: 289 loop : -1.11 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 448 TYR 0.037 0.002 TYR D 390 PHE 0.054 0.002 PHE M 131 TRP 0.031 0.001 TRP L 217 HIS 0.013 0.001 HIS F 331 Details of bonding type rmsd covalent geometry : bond 0.00360 (36088) covalent geometry : angle 0.72547 (49115) hydrogen bonds : bond 0.04079 ( 1909) hydrogen bonds : angle 4.68121 ( 5502) metal coordination : bond 0.01337 ( 36) metal coordination : angle 8.59594 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12019.62 seconds wall clock time: 205 minutes 2.18 seconds (12302.18 seconds total)