Starting phenix.real_space_refine on Sat Mar 23 02:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyu_12654/03_2024/7nyu_12654_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35228 Number of models: 1 Model: "" Number of chains: 18 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: "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: {'GLN:plan1': 1, 'GLU:plan': 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: "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: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 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: "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: "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: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 268 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: "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 1478 SG CYS B 158 178.846 106.982 66.831 1.00 55.34 S ATOM 849 SG CYS B 64 176.794 100.819 66.746 1.00 76.96 S ATOM 843 SG CYS B 63 173.647 103.866 63.422 1.00 85.99 S ATOM 1261 SG CYS B 129 173.764 106.920 68.492 1.00 61.52 S ATOM 7262 SG CYS E 92 223.218 165.181 64.042 1.00 51.70 S ATOM 7296 SG CYS E 97 225.783 165.122 62.378 1.00 52.28 S ATOM 7575 SG CYS E 133 219.999 168.265 62.280 1.00 52.38 S ATOM 7601 SG CYS E 137 221.711 169.036 60.577 1.00 58.19 S ATOM 10602 SG CYS F 357 203.759 158.585 62.650 1.00 43.95 S ATOM 10582 SG CYS F 354 199.126 158.487 63.464 1.00 58.94 S ATOM 10923 SG CYS F 398 201.561 163.884 62.380 1.00 55.89 S ATOM 10558 SG CYS F 351 201.874 161.611 67.783 1.00 42.95 S ATOM 11517 SG CYS G 34 188.365 156.183 66.734 1.00 61.68 S ATOM 11619 SG CYS G 48 186.534 155.642 62.509 1.00 60.11 S ATOM 11768 SG CYS G 67 186.366 158.000 64.685 1.00 51.83 S ATOM 11517 SG CYS G 34 188.365 156.183 66.734 1.00 61.68 S ATOM 11593 SG CYS G 45 190.071 153.438 65.721 1.00 52.73 S ATOM 12499 SG CYS G 157 193.913 153.193 79.122 1.00 62.67 S ATOM 12451 SG CYS G 151 197.426 149.653 75.374 1.00 43.68 S ATOM 12470 SG CYS G 154 191.585 151.346 73.586 1.00 47.53 S ATOM 12847 SG CYS G 201 191.873 147.151 77.719 1.00 52.17 S ATOM 12076 SG CYS G 106 192.914 138.097 77.156 1.00 47.70 S ATOM 12056 SG CYS G 103 194.074 135.673 71.359 1.00 55.35 S ATOM 12116 SG CYS G 112 190.171 140.631 72.748 1.00 52.04 S ATOM 13072 SG CYS G 228 173.876 147.447 93.163 1.00 52.88 S ATOM 13096 SG CYS G 231 173.284 151.589 95.206 1.00 46.39 S ATOM 13120 SG CYS G 235 173.805 150.859 90.135 1.00 40.39 S ATOM 13072 SG CYS G 228 173.876 147.447 93.163 1.00 52.88 S ATOM 13120 SG CYS G 235 173.805 150.859 90.135 1.00 40.39 S ATOM 13357 SG CYS G 263 178.125 151.010 92.504 1.00 37.17 S ATOM 20945 SG CYS I 109 194.239 121.443 73.280 1.00 49.73 S ATOM 20568 SG CYS I 60 193.443 121.524 79.854 1.00 51.19 S ATOM 20608 SG CYS I 66 188.536 120.586 76.316 1.00 62.78 S ATOM 20586 SG CYS I 63 191.458 125.864 75.278 1.00 52.06 S ATOM 20631 SG CYS I 70 181.725 116.609 72.890 1.00 64.48 S ATOM 20898 SG CYS I 102 183.550 114.722 67.973 1.00 55.99 S ATOM 20873 SG CYS I 99 184.134 110.475 73.128 1.00 45.52 S ATOM 20916 SG CYS I 105 187.926 115.648 71.434 1.00 52.41 S Time building chain proxies: 17.63, per 1000 atoms: 0.50 Number of scatterers: 35228 At special positions: 0 Unit cell: (252.888, 214.338, 138.78, 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 - 3.50 Amino acid : False - 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: 14.99 Conformation dependent library (CDL) restraints added in 7.1 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="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 351 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 357 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 354 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb=" SF4 G1003 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " 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 " Number of angles added : 95 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... running ksdssp... Secondary structure from input PDB file: 196 helices and 23 sheets defined 52.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.695A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.751A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.618A pdb=" N LEU D 53 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 140 removed outlier: 4.064A pdb=" N TRP D 132 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 140 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.854A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.805A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.836A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 270' Processing helix chain 'D' and resid 277 through 291 Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 331 through 349 removed outlier: 4.029A pdb=" N GLU D 347 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 395 Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 434 through 437 No H-bonds generated for 'chain 'D' and resid 434 through 437' Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 459 through 482 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 560 through 571 removed outlier: 3.882A pdb=" N ILE D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Proline residue: D 569 - end of helix Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.798A pdb=" N HIS E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.615A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.909A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 165 Proline residue: E 159 - end of helix Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.667A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.836A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 239 removed outlier: 4.000A pdb=" N ASN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE F 239 " --> pdb=" O TRP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 373 removed outlier: 3.816A 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 380 through 391 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 82 through 98 removed outlier: 4.909A pdb=" N ASN G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 195 through 200 Processing helix chain 'G' and resid 209 through 213 Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 264 through 268 Processing helix chain 'G' and resid 271 through 274 Processing helix chain 'G' and resid 295 through 308 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 343 through 358 Processing helix chain 'G' and resid 368 through 371 Processing helix chain 'G' and resid 387 through 407 removed outlier: 3.635A pdb=" N GLY G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS G 400 " --> pdb=" O ALA G 396 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 422 Processing helix chain 'G' and resid 451 through 465 Processing helix chain 'G' and resid 477 through 491 Processing helix chain 'G' and resid 502 through 504 No H-bonds generated for 'chain 'G' and resid 502 through 504' Processing helix chain 'G' and resid 507 through 522 Processing helix chain 'G' and resid 538 through 544 Processing helix chain 'G' and resid 549 through 557 Processing helix chain 'G' and resid 577 through 586 Processing helix chain 'G' and resid 599 through 601 No H-bonds generated for 'chain 'G' and resid 599 through 601' Processing helix chain 'G' and resid 613 through 615 No H-bonds generated for 'chain 'G' and resid 613 through 615' Processing helix chain 'G' and resid 648 through 661 Processing helix chain 'G' and resid 669 through 679 Processing helix chain 'G' and resid 681 through 689 removed outlier: 5.104A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 762 through 768 Processing helix chain 'G' and resid 825 through 827 No H-bonds generated for 'chain 'G' and resid 825 through 827' Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 844 through 850 Processing helix chain 'G' and resid 893 through 895 No H-bonds generated for 'chain 'G' and resid 893 through 895' Processing helix chain 'H' and resid 57 through 67 Processing helix chain 'H' and resid 81 through 100 Proline residue: H 87 - end of helix removed outlier: 3.640A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 137 removed outlier: 4.409A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 156 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.135A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 232 through 255 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 299 Processing helix chain 'H' and resid 304 through 320 removed outlier: 3.725A pdb=" N LEU H 308 " --> pdb=" O ILE H 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 58 removed outlier: 4.261A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 90 through 113 removed outlier: 3.680A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.902A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.733A pdb=" N ILE J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 158 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 59 through 86 removed outlier: 4.155A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 removed outlier: 4.230A pdb=" N ILE L 9 " --> pdb=" O LEU L 6 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 removed outlier: 4.015A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 removed outlier: 3.676A 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: 4.062A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 132 removed outlier: 3.801A pdb=" N ASN L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 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: 4.486A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 184 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 removed outlier: 4.277A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 241 through 244 Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 262 through 268 removed outlier: 3.566A pdb=" N ILE L 266 " --> pdb=" O GLY L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 291 removed outlier: 3.711A pdb=" N VAL L 283 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 300 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 removed outlier: 4.078A pdb=" N PHE L 340 " --> pdb=" O MET L 336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.565A 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) Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 396 through 409 Processing helix chain 'L' and resid 412 through 436 removed outlier: 4.349A pdb=" N PHE L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG L 431 " --> pdb=" O LEU L 427 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 464 Proline residue: L 456 - end of helix Processing helix chain 'L' and resid 466 through 470 removed outlier: 3.549A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 466 through 470' Processing helix chain 'L' and resid 490 through 513 Processing helix chain 'L' and resid 517 through 522 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 547 Processing helix chain 'L' and resid 550 through 559 Processing helix chain 'L' and resid 564 through 568 Processing helix chain 'L' and resid 571 through 586 Processing helix chain 'L' and resid 591 through 610 Processing helix chain 'M' and resid 2 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 27 through 49 removed outlier: 3.522A pdb=" N ILE M 34 " --> pdb=" O TRP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 114 through 131 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 149 through 158 Processing helix chain 'M' and resid 164 through 166 No H-bonds generated for 'chain 'M' and resid 164 through 166' Processing helix chain 'M' and resid 170 through 199 removed outlier: 3.822A pdb=" N THR M 178 " --> pdb=" O PHE M 174 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 220 through 232 removed outlier: 3.868A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 250 Processing helix chain 'M' and resid 253 through 261 Processing helix chain 'M' and resid 265 through 273 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 312 through 330 removed outlier: 3.986A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 4.271A 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 335 through 366 removed outlier: 3.530A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU M 355 " --> pdb=" O SER M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 removed outlier: 4.759A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 450 No H-bonds generated for 'chain 'M' and resid 448 through 450' Processing helix chain 'M' and resid 452 through 455 removed outlier: 3.531A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 452 through 455' Processing helix chain 'M' and resid 462 through 480 removed outlier: 3.718A pdb=" N LEU M 471 " --> pdb=" O MET M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 483 through 502 removed outlier: 5.119A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 removed outlier: 3.589A pdb=" N GLY N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 57 removed outlier: 4.105A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 removed outlier: 3.539A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) Proline residue: N 93 - end of helix removed outlier: 4.605A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 119 Processing helix chain 'N' and resid 125 through 141 removed outlier: 3.575A 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 152 through 178 removed outlier: 3.698A pdb=" N TYR N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 215 Processing helix chain 'N' and resid 221 through 233 removed outlier: 3.972A pdb=" N HIS N 224 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU N 225 " --> pdb=" O PRO N 222 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP N 226 " --> pdb=" O PHE N 223 " (cutoff:3.500A) Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 236 through 260 removed outlier: 3.613A pdb=" N PHE N 241 " --> pdb=" O PRO N 237 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) 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: 3.696A pdb=" N PHE N 258 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 285 removed outlier: 3.886A pdb=" N VAL N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 315 removed outlier: 3.825A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 347 Processing helix chain 'N' and resid 370 through 382 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.655A 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: 3.603A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 481 Processing sheet with id= A, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.765A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 44 through 47 removed outlier: 6.656A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.984A pdb=" N THR D 144 " --> pdb=" O VAL D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 212 through 214 removed outlier: 3.852A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 528 through 534 Processing sheet with id= F, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.465A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 86 through 91 removed outlier: 6.856A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 260 through 265 Processing sheet with id= I, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= J, first strand: chain 'G' and resid 62 through 65 removed outlier: 4.668A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 144 through 146 Processing sheet with id= L, first strand: chain 'G' and resid 171 through 173 Processing sheet with id= M, first strand: chain 'G' and resid 222 through 227 removed outlier: 3.591A pdb=" N ALA G 224 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 248 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG G 242 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 282 through 286 Processing sheet with id= O, first strand: chain 'G' and resid 312 through 315 removed outlier: 6.430A pdb=" N ALA G 563 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE G 315 " --> pdb=" O ALA G 563 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU G 589 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL G 566 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU G 606 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP G 594 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU G 608 " --> pdb=" O ASP G 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 445 through 448 removed outlier: 7.066A pdb=" N VAL G 375 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR G 432 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL G 377 " --> pdb=" O THR G 432 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY G 501 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY G 528 " --> pdb=" O ILE G 498 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER G 500 " --> pdb=" O GLY G 528 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR G 530 " --> pdb=" O SER G 500 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 621 Processing sheet with id= R, first strand: chain 'G' and resid 811 through 815 Processing sheet with id= S, first strand: chain 'G' and resid 839 through 842 removed outlier: 8.541A pdb=" N ILE G 840 " --> pdb=" O THR G 868 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU G 842 " --> pdb=" O PRO G 870 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU G 872 " --> pdb=" O LEU G 842 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 47 through 50 Processing sheet with id= U, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.772A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= W, first strand: chain 'L' and resid 66 through 70 removed outlier: 7.212A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) 1639 hydrogen bonds defined for protein. 4638 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: 11.37 Time building geometry restraints manager: 15.90 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: 15288 1.43 - 1.65: 20342 1.65 - 1.86: 365 1.86 - 2.07: 1 2.07 - 2.29: 92 Bond restraints: 36088 Sorted by residual: bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+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 E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.762 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N GLY B 191 " pdb=" CA GLY B 191 " ideal model delta sigma weight residual 1.449 1.479 -0.030 1.45e-02 4.76e+03 4.28e+00 bond pdb=" N CSX F 215 " pdb=" CA CSX F 215 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.36e+00 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 73.42 - 85.55: 88 85.55 - 97.67: 2 97.67 - 109.80: 5550 109.80 - 121.93: 36718 121.93 - 134.06: 6757 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 113.90 120.46 -6.56 1.80e+00 3.09e-01 1.33e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.51 4.86 1.34e+00 5.57e-01 1.32e+01 angle pdb=" CA PHE L 341 " pdb=" CB PHE L 341 " pdb=" CG PHE L 341 " ideal model delta sigma weight residual 113.80 117.10 -3.30 1.00e+00 1.00e+00 1.09e+01 angle pdb=" N VAL N 221 " pdb=" CA VAL N 221 " pdb=" C VAL N 221 " ideal model delta sigma weight residual 108.88 115.92 -7.04 2.16e+00 2.14e-01 1.06e+01 angle pdb=" CA CYS G 228 " pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " ideal model delta sigma weight residual 114.40 121.41 -7.01 2.30e+00 1.89e-01 9.28e+00 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 20682 34.18 - 68.35: 391 68.35 - 102.53: 29 102.53 - 136.71: 0 136.71 - 170.88: 1 Dihedral angle restraints: 21103 sinusoidal: 7915 harmonic: 13188 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 86.71 170.88 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA TRP L 535 " pdb=" C TRP L 535 " pdb=" N TYR L 536 " pdb=" CA TYR L 536 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 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 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 21100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4270 0.052 - 0.104: 1089 0.104 - 0.157: 177 0.157 - 0.209: 15 0.209 - 0.261: 3 Chirality restraints: 5554 Sorted by residual: chirality pdb=" CA PHE L 341 " pdb=" N PHE L 341 " pdb=" C PHE L 341 " pdb=" CB PHE L 341 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL L 35 " pdb=" CA VAL L 35 " pdb=" CG1 VAL L 35 " pdb=" CG2 VAL L 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU L 299 " pdb=" CB LEU L 299 " pdb=" CD1 LEU L 299 " pdb=" CD2 LEU L 299 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5551 not shown) Planarity restraints: 6255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 356 " 0.021 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C PRO F 356 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO F 356 " 0.026 2.00e-02 2.50e+03 pdb=" N CYS F 357 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU G 457 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU G 457 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY G 458 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 30 " 0.031 2.00e-02 2.50e+03 2.31e-02 1.34e+01 pdb=" CG TRP M 30 " -0.061 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 " 0.020 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 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP M 30 " 0.004 2.00e-02 2.50e+03 ... (remaining 6252 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 454 2.66 - 3.22: 33779 3.22 - 3.78: 55648 3.78 - 4.34: 76205 4.34 - 4.90: 123842 Nonbonded interactions: 289928 Sorted by model distance: nonbonded pdb=" OG SER D 100 " pdb=" OD1 ASP D 102 " model vdw 2.097 2.440 nonbonded pdb=" OE2 GLU G 647 " pdb="CA CA G1005 " model vdw 2.184 2.510 nonbonded pdb=" NH2 ARG E 125 " pdb=" O TYR E 165 " model vdw 2.196 2.520 nonbonded pdb=" NH1 ARG A 63 " pdb=" O ASP D 210 " model vdw 2.196 2.520 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.217 2.520 ... (remaining 289923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.040 Extract box with map and model: 5.540 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 97.760 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.130 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36088 Z= 0.341 Angle : 0.855 8.522 49115 Z= 0.453 Chirality : 0.047 0.261 5554 Planarity : 0.006 0.083 6255 Dihedral : 13.976 170.882 12663 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.82 % Allowed : 2.83 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 4573 helix: -0.91 (0.09), residues: 2470 sheet: -0.36 (0.29), residues: 311 loop : -1.35 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP M 30 HIS 0.011 0.002 HIS F 400 PHE 0.046 0.003 PHE N 396 TYR 0.054 0.003 TYR N 397 ARG 0.011 0.001 ARG G 597 *********************** 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 1406 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1377 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.7433 (mp) cc_final: 0.6793 (mt) REVERT: D 141 PHE cc_start: 0.6907 (m-80) cc_final: 0.6286 (m-80) REVERT: D 255 MET cc_start: 0.7378 (tpp) cc_final: 0.7097 (tpp) REVERT: D 281 MET cc_start: 0.7285 (tpp) cc_final: 0.7058 (tpp) REVERT: D 301 VAL cc_start: 0.8589 (t) cc_final: 0.8130 (m) REVERT: D 417 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6181 (tp30) REVERT: D 485 PRO cc_start: 0.4439 (Cg_endo) cc_final: 0.4182 (Cg_exo) REVERT: D 509 GLU cc_start: 0.8153 (pm20) cc_final: 0.7206 (mp0) REVERT: E 75 PHE cc_start: 0.9275 (t80) cc_final: 0.9072 (t80) REVERT: E 161 LEU cc_start: 0.7249 (tp) cc_final: 0.6012 (mm) REVERT: F 53 GLN cc_start: 0.7492 (mt0) cc_final: 0.6934 (tp-100) REVERT: F 71 LEU cc_start: 0.7636 (tt) cc_final: 0.7244 (tp) REVERT: F 89 CYS cc_start: 0.8373 (t) cc_final: 0.6887 (p) REVERT: F 212 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8189 (mmtm) REVERT: F 235 TRP cc_start: 0.5889 (t60) cc_final: 0.5033 (t-100) REVERT: F 274 LEU cc_start: 0.8366 (tp) cc_final: 0.8033 (tp) REVERT: F 291 GLN cc_start: 0.4384 (mt0) cc_final: 0.4037 (mt0) REVERT: F 349 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6599 (mm-30) REVERT: F 437 GLN cc_start: 0.7037 (mt0) cc_final: 0.6601 (mt0) REVERT: G 17 ASP cc_start: 0.5298 (m-30) cc_final: 0.3713 (m-30) REVERT: G 245 GLU cc_start: 0.6972 (pt0) cc_final: 0.6155 (pt0) REVERT: G 299 MET cc_start: 0.6472 (mmp) cc_final: 0.5766 (ttm) REVERT: G 326 PHE cc_start: 0.7040 (t80) cc_final: 0.6400 (t80) REVERT: G 424 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.7301 (ptp-170) REVERT: G 435 ASP cc_start: 0.6996 (t0) cc_final: 0.6345 (t0) REVERT: G 453 ASP cc_start: 0.7026 (m-30) cc_final: 0.6359 (m-30) REVERT: G 589 LEU cc_start: 0.8202 (tp) cc_final: 0.7154 (tt) REVERT: G 624 GLU cc_start: 0.5448 (tt0) cc_final: 0.5107 (mm-30) REVERT: G 644 VAL cc_start: 0.7354 (t) cc_final: 0.6694 (t) REVERT: G 654 SER cc_start: 0.8190 (t) cc_final: 0.7769 (p) REVERT: G 658 THR cc_start: 0.8660 (m) cc_final: 0.8056 (t) REVERT: G 731 ASP cc_start: 0.7590 (m-30) cc_final: 0.7388 (m-30) REVERT: G 842 LEU cc_start: 0.8070 (mt) cc_final: 0.7798 (mt) REVERT: G 849 LYS cc_start: 0.7334 (ptpp) cc_final: 0.6457 (tmmt) REVERT: H 236 LEU cc_start: 0.6693 (mp) cc_final: 0.6028 (tp) REVERT: H 265 LEU cc_start: 0.5450 (pp) cc_final: 0.3973 (mt) REVERT: I 53 ASP cc_start: 0.6479 (t70) cc_final: 0.6160 (t0) REVERT: I 101 PHE cc_start: 0.7879 (m-80) cc_final: 0.7665 (m-80) REVERT: I 124 GLU cc_start: 0.8195 (tp30) cc_final: 0.7933 (mm-30) REVERT: J 64 MET cc_start: 0.7343 (mmm) cc_final: 0.7133 (tpp) REVERT: K 2 ILE cc_start: 0.1437 (mm) cc_final: 0.1168 (mm) REVERT: L 1 MET cc_start: -0.1084 (ptt) cc_final: -0.2841 (ptt) REVERT: L 73 PHE cc_start: 0.5110 (t80) cc_final: 0.4886 (t80) REVERT: L 214 MET cc_start: 0.0095 (ppp) cc_final: -0.1897 (pmm) REVERT: L 554 LEU cc_start: 0.6852 (mm) cc_final: 0.5299 (tp) REVERT: M 72 ILE cc_start: 0.7957 (mt) cc_final: 0.7660 (mm) REVERT: M 118 LEU cc_start: 0.2383 (pp) cc_final: 0.1558 (tp) REVERT: M 156 LEU cc_start: 0.5676 (tp) cc_final: 0.5247 (tp) REVERT: M 195 VAL cc_start: 0.7051 (m) cc_final: 0.6676 (p) REVERT: N 21 VAL cc_start: 0.7414 (t) cc_final: 0.6608 (t) REVERT: N 74 MET cc_start: 0.3162 (mtp) cc_final: 0.1825 (mtt) REVERT: N 125 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7208 (mp) REVERT: N 174 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5603 (ttt) REVERT: N 184 LEU cc_start: 0.7994 (mp) cc_final: 0.7270 (mp) REVERT: N 185 SER cc_start: 0.7387 (t) cc_final: 0.7177 (t) REVERT: N 283 PHE cc_start: 0.7292 (m-80) cc_final: 0.6825 (m-80) REVERT: N 379 MET cc_start: 0.5583 (mmt) cc_final: 0.4315 (mmm) REVERT: N 396 PHE cc_start: 0.7544 (t80) cc_final: 0.7292 (t80) outliers start: 29 outliers final: 7 residues processed: 1394 average time/residue: 0.4992 time to fit residues: 1087.8851 Evaluate side-chains 1079 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1069 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 174 MET 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 385 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 191 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 357 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 266 optimal weight: 0.0270 chunk 414 optimal weight: 8.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 232 GLN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 GLN E 78 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN G 123 HIS G 254 ASN G 747 HIS H 152 GLN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS K 84 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS M 361 GLN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS N 232 GLN ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36088 Z= 0.204 Angle : 0.663 13.070 49115 Z= 0.337 Chirality : 0.042 0.171 5554 Planarity : 0.005 0.064 6255 Dihedral : 5.821 174.429 5003 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.78 % Allowed : 15.19 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4573 helix: 0.03 (0.10), residues: 2483 sheet: -0.00 (0.29), residues: 328 loop : -1.05 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 143 HIS 0.025 0.001 HIS M 322 PHE 0.034 0.002 PHE B 59 TYR 0.032 0.002 TYR M 435 ARG 0.009 0.001 ARG F 39 *********************** 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 1211 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1113 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 PHE cc_start: 0.7629 (t80) cc_final: 0.7243 (t80) REVERT: B 136 TYR cc_start: 0.7075 (m-80) cc_final: 0.6809 (m-80) REVERT: B 159 PRO cc_start: 0.9032 (Cg_endo) cc_final: 0.8765 (Cg_exo) REVERT: B 170 MET cc_start: 0.7058 (mtp) cc_final: 0.6368 (mpp) REVERT: B 197 MET cc_start: 0.4570 (mpp) cc_final: 0.4011 (mpp) REVERT: D 78 GLU cc_start: 0.6016 (tt0) cc_final: 0.5706 (mm-30) REVERT: D 132 TRP cc_start: 0.6810 (m-10) cc_final: 0.6218 (m-10) REVERT: D 141 PHE cc_start: 0.6673 (m-80) cc_final: 0.6296 (m-80) REVERT: D 228 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5480 (mtp85) REVERT: D 436 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7451 (mtmt) REVERT: D 468 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: D 509 GLU cc_start: 0.7944 (pm20) cc_final: 0.7512 (mp0) REVERT: E 99 ILE cc_start: 0.7668 (mm) cc_final: 0.7437 (tt) REVERT: E 161 LEU cc_start: 0.7019 (tp) cc_final: 0.6112 (tp) REVERT: F 43 THR cc_start: 0.6056 (p) cc_final: 0.5750 (t) REVERT: F 53 GLN cc_start: 0.7637 (mt0) cc_final: 0.7007 (tp-100) REVERT: F 224 ASN cc_start: 0.8353 (m-40) cc_final: 0.7968 (m-40) REVERT: F 235 TRP cc_start: 0.5941 (t60) cc_final: 0.5274 (t-100) REVERT: F 236 TYR cc_start: 0.6358 (t80) cc_final: 0.5700 (t80) REVERT: F 237 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.5803 (tm-30) REVERT: F 291 GLN cc_start: 0.4197 (mt0) cc_final: 0.3855 (mt0) REVERT: F 386 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7258 (mm-40) REVERT: G 68 MET cc_start: 0.8068 (mmm) cc_final: 0.7747 (mmm) REVERT: G 299 MET cc_start: 0.6662 (mmp) cc_final: 0.5993 (ttm) REVERT: G 326 PHE cc_start: 0.7335 (t80) cc_final: 0.6595 (t80) REVERT: G 408 GLN cc_start: 0.7625 (tp-100) cc_final: 0.7358 (tp-100) REVERT: G 420 ASN cc_start: 0.7460 (t0) cc_final: 0.7078 (t0) REVERT: G 424 ARG cc_start: 0.7407 (ptp-170) cc_final: 0.6855 (ptp-170) REVERT: G 432 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7250 (m) REVERT: G 434 VAL cc_start: 0.9123 (m) cc_final: 0.8920 (p) REVERT: G 440 ASP cc_start: 0.6563 (m-30) cc_final: 0.6356 (m-30) REVERT: G 453 ASP cc_start: 0.7075 (m-30) cc_final: 0.6439 (m-30) REVERT: G 454 GLN cc_start: 0.7358 (mt0) cc_final: 0.7136 (mt0) REVERT: G 551 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6639 (mp0) REVERT: G 640 ASP cc_start: 0.7508 (t0) cc_final: 0.6866 (t0) REVERT: G 654 SER cc_start: 0.8271 (t) cc_final: 0.7598 (p) REVERT: G 658 THR cc_start: 0.8481 (m) cc_final: 0.7938 (t) REVERT: G 741 ASN cc_start: 0.5788 (t0) cc_final: 0.5478 (t0) REVERT: G 849 LYS cc_start: 0.7011 (ptpp) cc_final: 0.6251 (tmmt) REVERT: G 900 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (mt) REVERT: H 131 LEU cc_start: 0.7557 (mt) cc_final: 0.7003 (mt) REVERT: H 236 LEU cc_start: 0.6537 (mp) cc_final: 0.5634 (tp) REVERT: H 267 PRO cc_start: 0.7361 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: I 101 PHE cc_start: 0.7927 (m-80) cc_final: 0.7686 (m-80) REVERT: I 124 GLU cc_start: 0.8160 (tp30) cc_final: 0.7917 (mm-30) REVERT: L 214 MET cc_start: 0.0956 (ppp) cc_final: -0.1091 (pmm) REVERT: L 243 MET cc_start: 0.1720 (mmm) cc_final: 0.1312 (ptp) REVERT: L 609 LEU cc_start: 0.3970 (mt) cc_final: 0.3648 (tp) REVERT: M 42 LEU cc_start: 0.6855 (tp) cc_final: 0.6036 (tp) REVERT: M 54 LEU cc_start: 0.3152 (pt) cc_final: 0.0425 (tp) REVERT: M 131 PHE cc_start: 0.5969 (m-10) cc_final: 0.5624 (m-10) REVERT: M 189 ILE cc_start: 0.6608 (mt) cc_final: 0.6338 (mt) REVERT: M 195 VAL cc_start: 0.7125 (m) cc_final: 0.6737 (p) REVERT: M 205 PHE cc_start: 0.5052 (m-10) cc_final: 0.4585 (m-10) REVERT: M 225 LEU cc_start: 0.7028 (mt) cc_final: 0.6729 (mp) REVERT: M 345 MET cc_start: 0.4824 (mmm) cc_final: 0.4484 (mmm) REVERT: M 370 ASP cc_start: 0.5195 (p0) cc_final: 0.3806 (p0) REVERT: N 52 LEU cc_start: 0.6111 (tp) cc_final: 0.5780 (tt) REVERT: N 55 VAL cc_start: 0.5873 (p) cc_final: 0.5541 (m) REVERT: N 74 MET cc_start: 0.2903 (mtp) cc_final: 0.2175 (mtt) REVERT: N 169 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6459 (t80) REVERT: N 260 TYR cc_start: 0.6737 (m-10) cc_final: 0.6377 (m-80) REVERT: N 297 LEU cc_start: 0.8121 (tt) cc_final: 0.7865 (tt) REVERT: N 359 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5636 (tt) REVERT: N 379 MET cc_start: 0.4704 (mmt) cc_final: 0.3349 (mmt) REVERT: N 396 PHE cc_start: 0.7620 (t80) cc_final: 0.7313 (t80) REVERT: N 427 ARG cc_start: 0.7239 (mmp80) cc_final: 0.6228 (ttp80) outliers start: 98 outliers final: 49 residues processed: 1145 average time/residue: 0.4760 time to fit residues: 872.0194 Evaluate side-chains 1071 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1015 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 590 TYR Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 361 GLN Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain N residue 169 PHE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 344 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 114 optimal weight: 0.0060 chunk 414 optimal weight: 4.9990 chunk 448 optimal weight: 0.5980 chunk 369 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 213 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 107 GLN F 172 HIS ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS G 138 GLN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN G 503 ASN G 653 HIS G 671 HIS G 766 ASN G 769 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN K 59 GLN K 84 HIS L 135 ASN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS N 199 ASN N 406 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 36088 Z= 0.360 Angle : 0.747 13.542 49115 Z= 0.383 Chirality : 0.046 0.324 5554 Planarity : 0.005 0.074 6255 Dihedral : 5.857 173.594 4986 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.56 % Allowed : 17.91 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4573 helix: 0.30 (0.10), residues: 2481 sheet: -0.38 (0.28), residues: 331 loop : -1.08 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 143 HIS 0.016 0.002 HIS M 322 PHE 0.031 0.002 PHE N 186 TYR 0.032 0.003 TYR M 435 ARG 0.009 0.001 ARG L 577 *********************** 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 1206 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1045 time to evaluate : 4.078 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: A 78 PHE cc_start: 0.7302 (m-10) cc_final: 0.6867 (m-80) REVERT: B 106 MET cc_start: 0.8252 (tpt) cc_final: 0.8009 (tpt) REVERT: B 117 MET cc_start: 0.7054 (ppp) cc_final: 0.6705 (ppp) REVERT: B 173 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: B 197 MET cc_start: 0.5485 (mpp) cc_final: 0.5128 (mpp) REVERT: D 76 MET cc_start: 0.6119 (ttt) cc_final: 0.5321 (mmm) REVERT: D 141 PHE cc_start: 0.7106 (m-80) cc_final: 0.6733 (m-80) REVERT: D 199 GLU cc_start: 0.7573 (pm20) cc_final: 0.6873 (pm20) REVERT: D 228 ARG cc_start: 0.6373 (mtp85) cc_final: 0.5881 (mtp85) REVERT: D 410 TYR cc_start: 0.4334 (p90) cc_final: 0.3975 (p90) REVERT: D 436 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7443 (mttt) REVERT: D 464 MET cc_start: 0.6593 (tmm) cc_final: 0.6156 (tmm) REVERT: D 483 ASN cc_start: 0.6796 (t0) cc_final: 0.6339 (m-40) REVERT: E 81 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.8024 (mmm160) REVERT: E 100 ASN cc_start: 0.7312 (m-40) cc_final: 0.6879 (m-40) REVERT: F 15 TRP cc_start: 0.7509 (p-90) cc_final: 0.2437 (t60) REVERT: F 25 TRP cc_start: 0.6919 (m100) cc_final: 0.6663 (m100) REVERT: F 53 GLN cc_start: 0.7796 (mt0) cc_final: 0.7067 (tp-100) REVERT: F 132 LEU cc_start: 0.8703 (tp) cc_final: 0.8469 (tp) REVERT: F 133 ARG cc_start: 0.8139 (ttt-90) cc_final: 0.7845 (ttt-90) REVERT: F 212 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8299 (mmtm) REVERT: F 236 TYR cc_start: 0.6822 (t80) cc_final: 0.6314 (t80) REVERT: F 237 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.5837 (tm-30) REVERT: F 252 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.5679 (t80) REVERT: F 386 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7604 (mm-40) REVERT: G 99 HIS cc_start: 0.8506 (t70) cc_final: 0.8030 (t70) REVERT: G 148 MET cc_start: 0.8763 (tpp) cc_final: 0.8283 (tpp) REVERT: G 193 PHE cc_start: 0.8671 (m-80) cc_final: 0.8442 (m-10) REVERT: G 408 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7671 (tp-100) REVERT: G 420 ASN cc_start: 0.7547 (t0) cc_final: 0.7075 (t0) REVERT: G 432 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (m) REVERT: G 453 ASP cc_start: 0.7616 (m-30) cc_final: 0.7044 (m-30) REVERT: G 454 GLN cc_start: 0.7346 (mt0) cc_final: 0.7142 (mt0) REVERT: G 570 ASP cc_start: 0.7893 (t0) cc_final: 0.7647 (p0) REVERT: G 640 ASP cc_start: 0.7828 (t0) cc_final: 0.7055 (t0) REVERT: G 644 VAL cc_start: 0.7046 (t) cc_final: 0.6397 (t) REVERT: G 671 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5447 (t-90) REVERT: G 706 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8646 (Cg_endo) REVERT: G 760 ASN cc_start: 0.8137 (m-40) cc_final: 0.7848 (m-40) REVERT: G 841 LYS cc_start: 0.6436 (mmmm) cc_final: 0.5760 (mmmt) REVERT: G 849 LYS cc_start: 0.7277 (ptpp) cc_final: 0.6354 (tmmt) REVERT: H 131 LEU cc_start: 0.7746 (mt) cc_final: 0.7154 (mt) REVERT: H 236 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5413 (tp) REVERT: H 298 MET cc_start: 0.4995 (ptp) cc_final: 0.3950 (ppp) REVERT: I 174 ASP cc_start: 0.5096 (t0) cc_final: 0.4877 (t0) REVERT: J 103 MET cc_start: 0.7026 (pmm) cc_final: 0.6600 (pmm) REVERT: K 53 TRP cc_start: 0.6457 (m100) cc_final: 0.6034 (m100) REVERT: K 98 MET cc_start: 0.1536 (mtm) cc_final: 0.0640 (mtp) REVERT: L 65 TRP cc_start: 0.4151 (p-90) cc_final: 0.3380 (p-90) REVERT: L 214 MET cc_start: 0.1528 (ppp) cc_final: 0.0173 (pmm) REVERT: L 243 MET cc_start: 0.2472 (mmm) cc_final: 0.2118 (ptp) REVERT: L 258 MET cc_start: -0.2980 (tmt) cc_final: -0.3785 (tmt) REVERT: M 54 LEU cc_start: 0.3489 (pt) cc_final: 0.1039 (tp) REVERT: M 69 MET cc_start: 0.7556 (ppp) cc_final: 0.5925 (mtt) REVERT: M 90 MET cc_start: 0.7016 (mmt) cc_final: 0.6812 (mmt) REVERT: M 112 TYR cc_start: 0.0442 (p90) cc_final: -0.0279 (p90) REVERT: M 131 PHE cc_start: 0.6027 (m-10) cc_final: 0.5621 (m-10) REVERT: M 189 ILE cc_start: 0.6563 (mt) cc_final: 0.6344 (mt) REVERT: M 195 VAL cc_start: 0.7079 (m) cc_final: 0.6635 (p) REVERT: M 222 LEU cc_start: 0.7226 (mp) cc_final: 0.5534 (tp) REVERT: M 382 LYS cc_start: 0.4903 (ptmm) cc_final: 0.4473 (mptt) REVERT: M 465 LEU cc_start: 0.2392 (mt) cc_final: 0.0553 (tp) REVERT: N 1 MET cc_start: 0.5930 (ppp) cc_final: 0.5592 (ppp) REVERT: N 25 MET cc_start: 0.7222 (ptp) cc_final: 0.6987 (tpt) REVERT: N 52 LEU cc_start: 0.6272 (tp) cc_final: 0.5901 (tt) REVERT: N 55 VAL cc_start: 0.5947 (p) cc_final: 0.5616 (m) REVERT: N 74 MET cc_start: 0.2438 (mtp) cc_final: 0.1601 (mtt) REVERT: N 260 TYR cc_start: 0.6982 (m-10) cc_final: 0.6658 (m-10) REVERT: N 297 LEU cc_start: 0.8450 (tt) cc_final: 0.8190 (tt) REVERT: N 379 MET cc_start: 0.5270 (mmt) cc_final: 0.5054 (tpp) REVERT: N 380 MET cc_start: 0.6849 (tmm) cc_final: 0.6348 (tmm) REVERT: N 396 PHE cc_start: 0.7665 (t80) cc_final: 0.7364 (t80) outliers start: 161 outliers final: 109 residues processed: 1106 average time/residue: 0.4840 time to fit residues: 865.5484 Evaluate side-chains 1101 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 986 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 440 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 394 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN D 163 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS F 341 ASN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN ** G 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS G 769 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 121 ASN L 338 HIS ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN M 416 GLN M 451 GLN N 199 ASN N 285 ASN N 406 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36088 Z= 0.205 Angle : 0.646 11.654 49115 Z= 0.325 Chirality : 0.042 0.211 5554 Planarity : 0.004 0.052 6255 Dihedral : 5.527 172.144 4986 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.62 % Allowed : 19.81 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 4573 helix: 0.56 (0.10), residues: 2492 sheet: -0.05 (0.29), residues: 323 loop : -0.98 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP L 143 HIS 0.011 0.001 HIS M 322 PHE 0.042 0.002 PHE L 578 TYR 0.027 0.002 TYR M 435 ARG 0.006 0.001 ARG G 698 *********************** 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 1176 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1013 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8219 (tpt) cc_final: 0.8011 (tpt) REVERT: B 117 MET cc_start: 0.7057 (ppp) cc_final: 0.6569 (ppp) REVERT: B 197 MET cc_start: 0.5662 (mpp) cc_final: 0.5379 (mpp) REVERT: B 204 LYS cc_start: 0.7603 (ptpt) cc_final: 0.7310 (ptpt) REVERT: D 141 PHE cc_start: 0.7154 (m-80) cc_final: 0.6908 (m-80) REVERT: D 199 GLU cc_start: 0.7316 (pm20) cc_final: 0.6488 (mm-30) REVERT: D 228 ARG cc_start: 0.6105 (mtp85) cc_final: 0.5712 (mtp85) REVERT: D 290 LEU cc_start: 0.8718 (mt) cc_final: 0.8420 (mt) REVERT: D 410 TYR cc_start: 0.4149 (p90) cc_final: 0.3888 (p90) REVERT: D 436 LYS cc_start: 0.7845 (mmtt) cc_final: 0.7334 (mttt) REVERT: D 464 MET cc_start: 0.6454 (tmm) cc_final: 0.5917 (tmm) REVERT: D 591 MET cc_start: 0.5510 (tpt) cc_final: 0.5271 (tpt) REVERT: F 15 TRP cc_start: 0.7413 (p-90) cc_final: 0.2759 (t60) REVERT: F 25 TRP cc_start: 0.6923 (m100) cc_final: 0.6678 (m100) REVERT: F 53 GLN cc_start: 0.7738 (mt0) cc_final: 0.6974 (tp-100) REVERT: F 94 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7200 (tpt) REVERT: F 237 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: F 252 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.5216 (t80) REVERT: F 262 TRP cc_start: 0.8094 (m-90) cc_final: 0.7435 (m-90) REVERT: F 386 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7662 (mm-40) REVERT: G 99 HIS cc_start: 0.8548 (t70) cc_final: 0.7816 (t70) REVERT: G 147 GLU cc_start: 0.5767 (mm-30) cc_final: 0.5476 (mm-30) REVERT: G 148 MET cc_start: 0.8659 (tpp) cc_final: 0.7956 (tpp) REVERT: G 181 PHE cc_start: 0.7972 (m-80) cc_final: 0.7432 (m-80) REVERT: G 408 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7555 (tp-100) REVERT: G 420 ASN cc_start: 0.7358 (t0) cc_final: 0.6995 (t0) REVERT: G 453 ASP cc_start: 0.7186 (m-30) cc_final: 0.6638 (m-30) REVERT: G 454 GLN cc_start: 0.7311 (mt0) cc_final: 0.6957 (mt0) REVERT: G 570 ASP cc_start: 0.7865 (t0) cc_final: 0.7662 (p0) REVERT: G 671 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5934 (t-90) REVERT: G 706 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8530 (Cg_endo) REVERT: G 734 PHE cc_start: 0.6811 (m-80) cc_final: 0.6499 (m-80) REVERT: G 767 LYS cc_start: 0.8471 (mppt) cc_final: 0.7913 (mptt) REVERT: G 841 LYS cc_start: 0.6421 (mmmm) cc_final: 0.5842 (mmmm) REVERT: G 849 LYS cc_start: 0.7150 (ptpp) cc_final: 0.6662 (tmtt) REVERT: H 131 LEU cc_start: 0.7664 (mt) cc_final: 0.7225 (mt) REVERT: H 236 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5431 (tp) REVERT: H 298 MET cc_start: 0.5269 (ptp) cc_final: 0.4206 (ppp) REVERT: I 145 TYR cc_start: 0.7150 (m-80) cc_final: 0.6635 (m-80) REVERT: J 103 MET cc_start: 0.7115 (pmm) cc_final: 0.6735 (pmm) REVERT: K 98 MET cc_start: 0.1917 (mtm) cc_final: 0.1007 (mtp) REVERT: L 143 TRP cc_start: 0.4886 (m100) cc_final: 0.4650 (m100) REVERT: L 169 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7610 (mtmm) REVERT: L 243 MET cc_start: 0.2820 (mmm) cc_final: 0.1342 (ptp) REVERT: L 258 MET cc_start: -0.3540 (tmt) cc_final: -0.4032 (tmt) REVERT: L 275 MET cc_start: -0.1545 (ttt) cc_final: -0.2352 (mtp) REVERT: M 54 LEU cc_start: 0.3351 (pt) cc_final: 0.0965 (tp) REVERT: M 69 MET cc_start: 0.7435 (ppp) cc_final: 0.6162 (mtt) REVERT: M 90 MET cc_start: 0.7010 (mmt) cc_final: 0.6759 (mmt) REVERT: M 131 PHE cc_start: 0.5779 (m-10) cc_final: 0.5395 (m-10) REVERT: M 195 VAL cc_start: 0.7019 (m) cc_final: 0.6644 (p) REVERT: M 225 LEU cc_start: 0.6953 (mt) cc_final: 0.6738 (mp) REVERT: M 457 LEU cc_start: -0.1881 (mp) cc_final: -0.2293 (mt) REVERT: N 1 MET cc_start: 0.5848 (ppp) cc_final: 0.5477 (ppp) REVERT: N 25 MET cc_start: 0.7351 (ptp) cc_final: 0.6874 (tpt) REVERT: N 52 LEU cc_start: 0.6170 (tp) cc_final: 0.5846 (mt) REVERT: N 55 VAL cc_start: 0.5803 (p) cc_final: 0.5480 (m) REVERT: N 74 MET cc_start: 0.2357 (mtp) cc_final: 0.1493 (mtt) REVERT: N 202 LEU cc_start: 0.4316 (mp) cc_final: 0.4114 (tp) REVERT: N 297 LEU cc_start: 0.8379 (tt) cc_final: 0.8148 (tt) REVERT: N 359 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5671 (tt) REVERT: N 380 MET cc_start: 0.6775 (tmm) cc_final: 0.6197 (tmm) REVERT: N 427 ARG cc_start: 0.7335 (mmp80) cc_final: 0.6028 (ttp80) outliers start: 163 outliers final: 111 residues processed: 1079 average time/residue: 0.4712 time to fit residues: 817.5167 Evaluate side-chains 1095 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 978 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 889 SER Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 169 PHE Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 376 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 225 optimal weight: 4.9990 chunk 395 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 172 HIS F 196 ASN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 ASN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN K 84 HIS L 121 ASN L 135 ASN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 36088 Z= 0.347 Angle : 0.737 14.423 49115 Z= 0.374 Chirality : 0.046 0.339 5554 Planarity : 0.005 0.059 6255 Dihedral : 5.855 173.407 4984 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.44 % Allowed : 20.83 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4573 helix: 0.56 (0.10), residues: 2457 sheet: -0.19 (0.29), residues: 334 loop : -1.12 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 143 HIS 0.010 0.002 HIS E 24 PHE 0.030 0.002 PHE L 578 TYR 0.029 0.002 TYR N 308 ARG 0.008 0.001 ARG G 159 *********************** 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 1207 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1015 time to evaluate : 3.439 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: B 117 MET cc_start: 0.6968 (ppp) cc_final: 0.6316 (ppp) REVERT: B 197 MET cc_start: 0.5706 (mpp) cc_final: 0.5018 (mpp) REVERT: D 95 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7243 (p90) REVERT: D 106 ASP cc_start: 0.7291 (m-30) cc_final: 0.7089 (m-30) REVERT: D 228 ARG cc_start: 0.6336 (mtp85) cc_final: 0.5895 (mtp85) REVERT: D 410 TYR cc_start: 0.4243 (p90) cc_final: 0.3878 (p90) REVERT: D 436 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7405 (mtmt) REVERT: D 460 TYR cc_start: 0.3456 (t80) cc_final: 0.3131 (t80) REVERT: D 464 MET cc_start: 0.6648 (tmm) cc_final: 0.6257 (tmm) REVERT: D 483 ASN cc_start: 0.7069 (t0) cc_final: 0.6437 (t0) REVERT: E 31 ASP cc_start: 0.7577 (t0) cc_final: 0.5237 (m-30) REVERT: F 15 TRP cc_start: 0.7702 (p-90) cc_final: 0.4409 (t60) REVERT: F 25 TRP cc_start: 0.7040 (m100) cc_final: 0.6816 (m100) REVERT: F 53 GLN cc_start: 0.8050 (mt0) cc_final: 0.7109 (tp-100) REVERT: F 94 MET cc_start: 0.7320 (tpp) cc_final: 0.6554 (tpt) REVERT: F 212 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8158 (mmtm) REVERT: F 237 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6385 (pm20) REVERT: F 252 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.5782 (t80) REVERT: F 262 TRP cc_start: 0.8216 (m-90) cc_final: 0.7398 (m-90) REVERT: F 285 LEU cc_start: 0.6471 (mp) cc_final: 0.6201 (mt) REVERT: F 371 LEU cc_start: 0.7572 (tt) cc_final: 0.7359 (tt) REVERT: F 441 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.4492 (tp) REVERT: G 68 MET cc_start: 0.8072 (mmm) cc_final: 0.7804 (mmm) REVERT: G 108 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: G 148 MET cc_start: 0.8677 (tpp) cc_final: 0.7802 (tpp) REVERT: G 366 LEU cc_start: 0.8918 (tp) cc_final: 0.8629 (tp) REVERT: G 408 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7647 (tp-100) REVERT: G 420 ASN cc_start: 0.7522 (t0) cc_final: 0.7272 (t0) REVERT: G 453 ASP cc_start: 0.7457 (m-30) cc_final: 0.7208 (m-30) REVERT: G 454 GLN cc_start: 0.7313 (mt0) cc_final: 0.7021 (mt0) REVERT: G 526 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5614 (m-30) REVERT: G 551 GLU cc_start: 0.6917 (mp0) cc_final: 0.6577 (mp0) REVERT: G 644 VAL cc_start: 0.7301 (t) cc_final: 0.6664 (t) REVERT: G 706 PRO cc_start: 0.8778 (Cg_exo) cc_final: 0.8556 (Cg_endo) REVERT: G 734 PHE cc_start: 0.7129 (m-80) cc_final: 0.6739 (m-80) REVERT: G 767 LYS cc_start: 0.8419 (mppt) cc_final: 0.7828 (mptt) REVERT: G 780 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7711 (p0) REVERT: G 846 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6989 (t0) REVERT: H 131 LEU cc_start: 0.7892 (mt) cc_final: 0.7267 (mt) REVERT: H 236 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5072 (tp) REVERT: H 237 PHE cc_start: 0.7917 (t80) cc_final: 0.7474 (t80) REVERT: H 298 MET cc_start: 0.5342 (ptp) cc_final: 0.4267 (ppp) REVERT: J 1 MET cc_start: 0.2953 (tpp) cc_final: 0.2335 (tpp) REVERT: J 103 MET cc_start: 0.7262 (pmm) cc_final: 0.6913 (pmm) REVERT: K 25 ARG cc_start: 0.6720 (tpm170) cc_final: 0.6503 (tpm170) REVERT: K 98 MET cc_start: 0.1834 (mtm) cc_final: 0.1305 (mtm) REVERT: L 1 MET cc_start: 0.1725 (ptt) cc_final: -0.1200 (ppp) REVERT: L 143 TRP cc_start: 0.4551 (m100) cc_final: 0.3644 (m100) REVERT: L 243 MET cc_start: 0.2912 (mmm) cc_final: 0.1269 (ptp) REVERT: L 258 MET cc_start: -0.3604 (tmt) cc_final: -0.4076 (tmt) REVERT: L 275 MET cc_start: -0.1157 (ttt) cc_final: -0.1868 (mtp) REVERT: L 587 GLU cc_start: 0.5699 (pt0) cc_final: 0.5431 (pt0) REVERT: M 54 LEU cc_start: 0.3547 (pt) cc_final: 0.1553 (mt) REVERT: M 69 MET cc_start: 0.7502 (ppp) cc_final: 0.6213 (mtt) REVERT: M 90 MET cc_start: 0.7061 (mmt) cc_final: 0.6720 (mmt) REVERT: M 131 PHE cc_start: 0.5874 (m-10) cc_final: 0.5477 (m-10) REVERT: M 185 MET cc_start: 0.4451 (ppp) cc_final: 0.4241 (ppp) REVERT: M 222 LEU cc_start: 0.7082 (mp) cc_final: 0.5388 (tp) REVERT: M 223 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.4578 (mt) REVERT: M 299 PHE cc_start: 0.6144 (m-10) cc_final: 0.5415 (m-10) REVERT: M 323 MET cc_start: 0.3468 (mmp) cc_final: 0.3045 (mmp) REVERT: N 25 MET cc_start: 0.7300 (ptp) cc_final: 0.6810 (tpt) REVERT: N 74 MET cc_start: 0.2361 (mtp) cc_final: 0.1536 (mtt) REVERT: N 178 TYR cc_start: 0.5163 (t80) cc_final: 0.4917 (t80) REVERT: N 204 LEU cc_start: 0.6314 (pp) cc_final: 0.5690 (mp) REVERT: N 260 TYR cc_start: 0.6896 (m-10) cc_final: 0.5738 (m-10) REVERT: N 287 MET cc_start: 0.3917 (tmm) cc_final: 0.3508 (tmm) REVERT: N 297 LEU cc_start: 0.8433 (tt) cc_final: 0.8206 (tt) REVERT: N 359 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5601 (tt) REVERT: N 379 MET cc_start: 0.6355 (tpp) cc_final: 0.5494 (tpp) REVERT: N 380 MET cc_start: 0.6851 (tmm) cc_final: 0.5926 (tmm) REVERT: N 397 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: N 427 ARG cc_start: 0.7311 (mmp80) cc_final: 0.6140 (ttp80) outliers start: 192 outliers final: 140 residues processed: 1099 average time/residue: 0.4651 time to fit residues: 822.9655 Evaluate side-chains 1118 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 966 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 ILE 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 261 LEU Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 640 ASP Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 780 ASP Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 846 ASP Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 889 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 441 optimal weight: 2.9990 chunk 366 optimal weight: 20.0000 chunk 204 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 196 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS M 339 GLN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 36088 Z= 0.355 Angle : 0.743 13.372 49115 Z= 0.379 Chirality : 0.047 0.385 5554 Planarity : 0.005 0.053 6255 Dihedral : 6.034 173.953 4984 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 5.92 % Allowed : 22.87 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4573 helix: 0.51 (0.10), residues: 2450 sheet: -0.56 (0.27), residues: 338 loop : -1.28 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP L 67 HIS 0.012 0.002 HIS G 259 PHE 0.029 0.002 PHE M 480 TYR 0.041 0.002 TYR N 308 ARG 0.010 0.001 ARG G 424 *********************** 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 1184 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 975 time to evaluate : 3.850 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: A 116 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.4069 (t80) REVERT: B 106 MET cc_start: 0.8156 (tpt) cc_final: 0.7868 (tpt) REVERT: B 170 MET cc_start: 0.7738 (mtp) cc_final: 0.7045 (mtp) REVERT: B 196 ASN cc_start: 0.6246 (OUTLIER) cc_final: 0.5726 (t0) REVERT: B 197 MET cc_start: 0.5716 (mpp) cc_final: 0.5158 (mpp) REVERT: D 95 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7299 (p90) REVERT: D 106 ASP cc_start: 0.7311 (m-30) cc_final: 0.7000 (m-30) REVERT: D 228 ARG cc_start: 0.6404 (mtp85) cc_final: 0.5997 (mtp85) REVERT: D 414 GLU cc_start: 0.6718 (mp0) cc_final: 0.6219 (tp30) REVERT: D 436 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7468 (mtmt) REVERT: D 447 ASP cc_start: 0.4704 (OUTLIER) cc_final: 0.3695 (p0) REVERT: D 460 TYR cc_start: 0.4255 (t80) cc_final: 0.3765 (t80) REVERT: D 483 ASN cc_start: 0.7183 (t0) cc_final: 0.6741 (m-40) REVERT: F 25 TRP cc_start: 0.7017 (m100) cc_final: 0.6729 (m100) REVERT: F 36 GLU cc_start: 0.7693 (mp0) cc_final: 0.7325 (pm20) REVERT: F 45 LEU cc_start: 0.6587 (mp) cc_final: 0.6361 (mt) REVERT: F 53 GLN cc_start: 0.8186 (mt0) cc_final: 0.6986 (tp-100) REVERT: F 94 MET cc_start: 0.7259 (tpp) cc_final: 0.6310 (tpt) REVERT: F 237 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6001 (tm-30) REVERT: F 252 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.5352 (t80) REVERT: F 285 LEU cc_start: 0.6498 (mp) cc_final: 0.6003 (mt) REVERT: F 371 LEU cc_start: 0.7568 (tt) cc_final: 0.7349 (tt) REVERT: F 413 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7821 (mttp) REVERT: F 441 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.4368 (tp) REVERT: G 41 SER cc_start: 0.8826 (p) cc_final: 0.8314 (p) REVERT: G 68 MET cc_start: 0.8135 (mmm) cc_final: 0.7918 (mmm) REVERT: G 108 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: G 148 MET cc_start: 0.8713 (tpp) cc_final: 0.8018 (tpp) REVERT: G 190 GLU cc_start: 0.7289 (mp0) cc_final: 0.7000 (mp0) REVERT: G 230 GLN cc_start: 0.7959 (mm110) cc_final: 0.7725 (mm-40) REVERT: G 245 GLU cc_start: 0.8470 (pm20) cc_final: 0.8239 (pm20) REVERT: G 366 LEU cc_start: 0.8973 (tp) cc_final: 0.8640 (tp) REVERT: G 408 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7588 (tp-100) REVERT: G 414 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: G 420 ASN cc_start: 0.7551 (t0) cc_final: 0.7306 (t0) REVERT: G 453 ASP cc_start: 0.7544 (m-30) cc_final: 0.7323 (m-30) REVERT: G 454 GLN cc_start: 0.7342 (mt0) cc_final: 0.6990 (mt0) REVERT: G 495 LYS cc_start: 0.8074 (mttt) cc_final: 0.7755 (mtmm) REVERT: G 526 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5516 (m-30) REVERT: G 589 LEU cc_start: 0.8419 (tp) cc_final: 0.8211 (tp) REVERT: G 644 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6659 (t) REVERT: G 671 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.5859 (t-90) REVERT: G 734 PHE cc_start: 0.7139 (m-80) cc_final: 0.6601 (m-80) REVERT: G 748 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7167 (pmt-80) REVERT: G 767 LYS cc_start: 0.8473 (mppt) cc_final: 0.8086 (mppt) REVERT: G 842 LEU cc_start: 0.8050 (mt) cc_final: 0.7760 (mt) REVERT: H 131 LEU cc_start: 0.7945 (mt) cc_final: 0.7347 (mt) REVERT: H 236 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5474 (tp) REVERT: H 267 PRO cc_start: 0.7450 (Cg_endo) cc_final: 0.7118 (Cg_exo) REVERT: H 298 MET cc_start: 0.4954 (ptp) cc_final: 0.4126 (ppp) REVERT: I 145 TYR cc_start: 0.6535 (m-80) cc_final: 0.6259 (m-80) REVERT: J 74 LEU cc_start: 0.8407 (mt) cc_final: 0.8037 (tt) REVERT: K 98 MET cc_start: 0.2057 (mtm) cc_final: 0.1451 (mtm) REVERT: L 1 MET cc_start: 0.2017 (ptt) cc_final: -0.1357 (tmm) REVERT: L 243 MET cc_start: 0.2981 (mmm) cc_final: 0.1251 (ptp) REVERT: L 258 MET cc_start: -0.3593 (tmt) cc_final: -0.4000 (tmt) REVERT: L 275 MET cc_start: -0.1615 (ttt) cc_final: -0.2215 (mtp) REVERT: L 305 LYS cc_start: 0.7388 (mmmm) cc_final: 0.7106 (mmmm) REVERT: M 15 PHE cc_start: 0.5036 (m-10) cc_final: 0.4709 (m-10) REVERT: M 48 LEU cc_start: 0.1906 (OUTLIER) cc_final: 0.1290 (tt) REVERT: M 54 LEU cc_start: 0.3576 (pt) cc_final: 0.2883 (pt) REVERT: M 69 MET cc_start: 0.7137 (ppp) cc_final: 0.6209 (mtt) REVERT: M 90 MET cc_start: 0.6478 (mmt) cc_final: 0.5803 (mmt) REVERT: M 222 LEU cc_start: 0.7206 (mp) cc_final: 0.5432 (tp) REVERT: M 223 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.4701 (mt) REVERT: M 306 PHE cc_start: 0.6851 (t80) cc_final: 0.4694 (t80) REVERT: M 323 MET cc_start: 0.3754 (mmp) cc_final: 0.2862 (mmp) REVERT: M 366 ILE cc_start: 0.3169 (pt) cc_final: 0.1855 (mm) REVERT: M 374 MET cc_start: 0.0563 (ttt) cc_final: -0.0127 (mtm) REVERT: M 468 ILE cc_start: 0.4515 (tt) cc_final: 0.4186 (pt) REVERT: N 25 MET cc_start: 0.7212 (ptp) cc_final: 0.6687 (tpt) REVERT: N 74 MET cc_start: 0.2364 (mtp) cc_final: 0.1454 (mtt) REVERT: N 176 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6588 (tt) REVERT: N 204 LEU cc_start: 0.6242 (pp) cc_final: 0.5672 (mp) REVERT: N 260 TYR cc_start: 0.6938 (m-10) cc_final: 0.5800 (m-10) REVERT: N 287 MET cc_start: 0.4302 (tmm) cc_final: 0.3794 (tmm) REVERT: N 297 LEU cc_start: 0.8425 (tt) cc_final: 0.8205 (tt) REVERT: N 359 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5538 (tt) REVERT: N 379 MET cc_start: 0.6346 (tpp) cc_final: 0.5324 (tpp) REVERT: N 397 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5959 (m-10) REVERT: N 427 ARG cc_start: 0.7245 (mmp80) cc_final: 0.6200 (ttp80) outliers start: 209 outliers final: 147 residues processed: 1080 average time/residue: 0.4768 time to fit residues: 821.5257 Evaluate side-chains 1107 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 941 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 ILE 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 261 LEU Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 640 ASP Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 671 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 862 TYR Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 67 TRP Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 605 VAL Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 376 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 408 TRP Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.6980 chunk 49 optimal weight: 0.0170 chunk 251 optimal weight: 0.6980 chunk 322 optimal weight: 8.9990 chunk 249 optimal weight: 0.7980 chunk 371 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 439 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 202 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 262 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS F 304 HIS F 341 ASN ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 121 ASN L 232 GLN M 198 ASN M 339 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36088 Z= 0.196 Angle : 0.676 12.736 49115 Z= 0.337 Chirality : 0.043 0.330 5554 Planarity : 0.004 0.057 6255 Dihedral : 5.606 170.913 4984 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 4.14 % Allowed : 25.23 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4573 helix: 0.77 (0.11), residues: 2473 sheet: -0.18 (0.29), residues: 302 loop : -1.07 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP L 143 HIS 0.012 0.001 HIS G 259 PHE 0.037 0.002 PHE L 578 TYR 0.038 0.002 TYR N 333 ARG 0.007 0.001 ARG G 159 *********************** 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 1145 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 999 time to evaluate : 3.685 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: A 116 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4150 (t80) REVERT: B 59 PHE cc_start: 0.7293 (t80) cc_final: 0.7063 (t80) REVERT: B 106 MET cc_start: 0.7901 (tpt) cc_final: 0.7607 (tpt) REVERT: B 170 MET cc_start: 0.7581 (mtp) cc_final: 0.6785 (mtp) REVERT: B 197 MET cc_start: 0.5365 (mpp) cc_final: 0.4787 (mpp) REVERT: D 76 MET cc_start: 0.5814 (ttt) cc_final: 0.5238 (mmt) REVERT: D 95 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7214 (p90) REVERT: D 96 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: D 106 ASP cc_start: 0.6794 (m-30) cc_final: 0.6454 (m-30) REVERT: D 139 ASP cc_start: 0.7617 (t0) cc_final: 0.7296 (t0) REVERT: D 199 GLU cc_start: 0.7612 (pm20) cc_final: 0.7379 (pm20) REVERT: D 228 ARG cc_start: 0.6175 (mtp85) cc_final: 0.5813 (mtp85) REVERT: D 290 LEU cc_start: 0.8775 (mt) cc_final: 0.8552 (mt) REVERT: D 436 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7330 (mttt) REVERT: D 483 ASN cc_start: 0.7113 (t0) cc_final: 0.6455 (t0) REVERT: D 558 ARG cc_start: 0.7109 (tpt-90) cc_final: 0.6850 (tmt-80) REVERT: F 11 HIS cc_start: 0.8093 (m90) cc_final: 0.7823 (m-70) REVERT: F 15 TRP cc_start: 0.7658 (p-90) cc_final: 0.4740 (t60) REVERT: F 36 GLU cc_start: 0.7353 (mp0) cc_final: 0.7066 (pm20) REVERT: F 53 GLN cc_start: 0.8073 (mt0) cc_final: 0.7096 (tp-100) REVERT: F 71 LEU cc_start: 0.8464 (tt) cc_final: 0.8183 (tp) REVERT: F 94 MET cc_start: 0.7974 (tpp) cc_final: 0.7017 (tpt) REVERT: F 237 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: F 252 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.5350 (t80) REVERT: F 262 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.7050 (m-90) REVERT: F 299 PHE cc_start: 0.7872 (m-80) cc_final: 0.7471 (m-80) REVERT: G 230 GLN cc_start: 0.7968 (mm110) cc_final: 0.7730 (mm-40) REVERT: G 260 TYR cc_start: 0.7979 (m-80) cc_final: 0.7759 (m-80) REVERT: G 408 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7455 (tp-100) REVERT: G 414 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: G 420 ASN cc_start: 0.7423 (t0) cc_final: 0.6802 (t0) REVERT: G 447 TYR cc_start: 0.8168 (t80) cc_final: 0.7905 (t80) REVERT: G 453 ASP cc_start: 0.7245 (m-30) cc_final: 0.7040 (m-30) REVERT: G 495 LYS cc_start: 0.8018 (mttt) cc_final: 0.7454 (mtmm) REVERT: G 629 ARG cc_start: 0.6486 (tpp80) cc_final: 0.5888 (tpp80) REVERT: G 644 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6523 (t) REVERT: G 734 PHE cc_start: 0.7031 (m-80) cc_final: 0.6701 (m-80) REVERT: G 842 LEU cc_start: 0.7979 (mt) cc_final: 0.7737 (mt) REVERT: G 846 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6993 (t70) REVERT: H 131 LEU cc_start: 0.7696 (mt) cc_final: 0.7268 (mt) REVERT: H 236 LEU cc_start: 0.5682 (mp) cc_final: 0.5007 (tp) REVERT: H 245 ILE cc_start: 0.4166 (tp) cc_final: 0.3916 (tp) REVERT: H 267 PRO cc_start: 0.7488 (Cg_endo) cc_final: 0.7197 (Cg_exo) REVERT: H 298 MET cc_start: 0.4904 (ptp) cc_final: 0.4130 (ppp) REVERT: I 145 TYR cc_start: 0.7158 (m-80) cc_final: 0.6613 (m-80) REVERT: J 74 LEU cc_start: 0.8464 (mt) cc_final: 0.8172 (tt) REVERT: K 31 MET cc_start: 0.5997 (mpp) cc_final: 0.5502 (tpp) REVERT: K 98 MET cc_start: 0.1992 (mtm) cc_final: 0.1307 (mtp) REVERT: L 1 MET cc_start: 0.2179 (ptt) cc_final: -0.1169 (tmm) REVERT: L 122 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5419 (mt) REVERT: L 243 MET cc_start: 0.2873 (mmm) cc_final: 0.1553 (ptp) REVERT: L 258 MET cc_start: -0.3002 (tmt) cc_final: -0.3534 (tmt) REVERT: L 275 MET cc_start: -0.1334 (ttt) cc_final: -0.1739 (mtp) REVERT: L 305 LYS cc_start: 0.7398 (mmmm) cc_final: 0.7190 (mmmm) REVERT: M 52 TYR cc_start: 0.4609 (p90) cc_final: 0.4393 (p90) REVERT: M 54 LEU cc_start: 0.3480 (pt) cc_final: 0.1848 (mt) REVERT: M 69 MET cc_start: 0.6590 (ppp) cc_final: 0.6192 (mtt) REVERT: M 90 MET cc_start: 0.6499 (mmt) cc_final: 0.5778 (mmt) REVERT: M 185 MET cc_start: 0.4410 (ppp) cc_final: 0.4205 (ppp) REVERT: M 222 LEU cc_start: 0.7295 (mp) cc_final: 0.6060 (tp) REVERT: M 223 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5010 (mt) REVERT: M 299 PHE cc_start: 0.5845 (m-10) cc_final: 0.5233 (m-10) REVERT: M 345 MET cc_start: 0.5500 (mmm) cc_final: 0.5246 (mmm) REVERT: M 366 ILE cc_start: 0.3164 (pt) cc_final: 0.1770 (mm) REVERT: M 374 MET cc_start: 0.1467 (ttt) cc_final: 0.0078 (mtm) REVERT: M 464 GLU cc_start: 0.1765 (mm-30) cc_final: 0.1410 (mm-30) REVERT: N 25 MET cc_start: 0.7162 (ptp) cc_final: 0.6623 (tpt) REVERT: N 74 MET cc_start: 0.2313 (mtp) cc_final: 0.1458 (mtt) REVERT: N 204 LEU cc_start: 0.6578 (pp) cc_final: 0.5980 (mp) REVERT: N 287 MET cc_start: 0.4110 (tmm) cc_final: 0.3840 (tmm) REVERT: N 297 LEU cc_start: 0.8317 (tt) cc_final: 0.8117 (tt) REVERT: N 359 LEU cc_start: 0.5734 (tt) cc_final: 0.5235 (tt) REVERT: N 379 MET cc_start: 0.6149 (tpp) cc_final: 0.5271 (tpp) REVERT: N 380 MET cc_start: 0.6534 (tmm) cc_final: 0.5828 (tmm) REVERT: N 397 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: N 427 ARG cc_start: 0.7167 (mmp80) cc_final: 0.6271 (ttp80) outliers start: 146 outliers final: 104 residues processed: 1072 average time/residue: 0.5077 time to fit residues: 875.4073 Evaluate side-chains 1069 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 953 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 TRP Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 846 ASP Chi-restraints excluded: chain G residue 862 TYR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 236 GLN Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 279 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 345 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 104 ASN ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 574 HIS H 181 ASN K 84 HIS L 121 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36088 Z= 0.209 Angle : 0.685 12.570 49115 Z= 0.341 Chirality : 0.043 0.305 5554 Planarity : 0.004 0.058 6255 Dihedral : 5.554 170.680 4984 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.08 % Allowed : 26.08 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.13), residues: 4573 helix: 0.82 (0.11), residues: 2469 sheet: -0.15 (0.29), residues: 302 loop : -1.07 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP L 67 HIS 0.021 0.001 HIS M 117 PHE 0.032 0.002 PHE M 480 TYR 0.037 0.002 TYR N 308 ARG 0.010 0.001 ARG G 159 *********************** 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 1121 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 977 time to evaluate : 3.667 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: A 116 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4191 (t80) REVERT: B 48 TRP cc_start: 0.6127 (OUTLIER) cc_final: 0.5762 (t60) REVERT: B 59 PHE cc_start: 0.7319 (t80) cc_final: 0.7013 (t80) REVERT: B 161 ARG cc_start: 0.6494 (mmm160) cc_final: 0.6254 (mmm160) REVERT: B 170 MET cc_start: 0.7468 (mtp) cc_final: 0.6672 (mtp) REVERT: B 196 ASN cc_start: 0.5171 (OUTLIER) cc_final: 0.4654 (t0) REVERT: B 197 MET cc_start: 0.5544 (mpp) cc_final: 0.5038 (mpp) REVERT: D 76 MET cc_start: 0.6066 (ttt) cc_final: 0.5386 (mmt) REVERT: D 95 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7221 (p90) REVERT: D 106 ASP cc_start: 0.7130 (m-30) cc_final: 0.6760 (m-30) REVERT: D 139 ASP cc_start: 0.7488 (t0) cc_final: 0.7211 (t0) REVERT: D 199 GLU cc_start: 0.7551 (pm20) cc_final: 0.7183 (pm20) REVERT: D 228 ARG cc_start: 0.6198 (mtp85) cc_final: 0.5895 (mtp85) REVERT: D 290 LEU cc_start: 0.8806 (mt) cc_final: 0.8577 (mt) REVERT: D 294 THR cc_start: 0.8795 (p) cc_final: 0.8572 (t) REVERT: D 436 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7177 (mtmt) REVERT: D 483 ASN cc_start: 0.7125 (t0) cc_final: 0.6450 (t0) REVERT: D 532 MET cc_start: 0.6898 (mmm) cc_final: 0.6607 (mmp) REVERT: F 11 HIS cc_start: 0.8281 (m90) cc_final: 0.8012 (m-70) REVERT: F 15 TRP cc_start: 0.7651 (p-90) cc_final: 0.4338 (t60) REVERT: F 36 GLU cc_start: 0.7440 (mp0) cc_final: 0.7106 (pm20) REVERT: F 53 GLN cc_start: 0.8088 (mt0) cc_final: 0.7137 (tp-100) REVERT: F 71 LEU cc_start: 0.8460 (tt) cc_final: 0.8192 (tp) REVERT: F 94 MET cc_start: 0.7990 (tpp) cc_final: 0.6979 (tpt) REVERT: F 252 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6071 (t80) REVERT: F 299 PHE cc_start: 0.7821 (m-80) cc_final: 0.7424 (m-80) REVERT: G 108 GLU cc_start: 0.6921 (tt0) cc_final: 0.6713 (tt0) REVERT: G 169 ASP cc_start: 0.8375 (p0) cc_final: 0.7993 (p0) REVERT: G 260 TYR cc_start: 0.8302 (m-80) cc_final: 0.7889 (m-80) REVERT: G 408 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7421 (tp-100) REVERT: G 414 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: G 420 ASN cc_start: 0.7374 (t0) cc_final: 0.7130 (t0) REVERT: G 447 TYR cc_start: 0.7871 (t80) cc_final: 0.7577 (t80) REVERT: G 453 ASP cc_start: 0.7209 (m-30) cc_final: 0.6935 (m-30) REVERT: G 495 LYS cc_start: 0.7790 (mttt) cc_final: 0.7305 (mtmm) REVERT: G 629 ARG cc_start: 0.6510 (tpp80) cc_final: 0.5903 (tpp80) REVERT: G 644 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6602 (t) REVERT: G 734 PHE cc_start: 0.6942 (m-80) cc_final: 0.6658 (m-80) REVERT: G 767 LYS cc_start: 0.8433 (mppt) cc_final: 0.8174 (mppt) REVERT: G 769 GLN cc_start: 0.6437 (mm-40) cc_final: 0.5994 (mm-40) REVERT: G 842 LEU cc_start: 0.7992 (mt) cc_final: 0.7741 (mt) REVERT: H 131 LEU cc_start: 0.7812 (mt) cc_final: 0.7299 (mt) REVERT: H 236 LEU cc_start: 0.5681 (mp) cc_final: 0.5039 (tp) REVERT: H 245 ILE cc_start: 0.4198 (tp) cc_final: 0.3927 (tp) REVERT: H 267 PRO cc_start: 0.7514 (Cg_endo) cc_final: 0.7251 (Cg_exo) REVERT: H 298 MET cc_start: 0.4812 (ptp) cc_final: 0.4057 (ppp) REVERT: J 74 LEU cc_start: 0.8478 (mt) cc_final: 0.8202 (tt) REVERT: K 25 ARG cc_start: 0.6549 (tpm170) cc_final: 0.6000 (tpm170) REVERT: K 31 MET cc_start: 0.5830 (mpp) cc_final: 0.5380 (tpp) REVERT: K 98 MET cc_start: 0.1995 (mtm) cc_final: 0.1446 (mtm) REVERT: L 1 MET cc_start: 0.2033 (ptt) cc_final: -0.1303 (tmm) REVERT: L 73 PHE cc_start: 0.5708 (t80) cc_final: 0.5482 (t80) REVERT: L 122 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5477 (mt) REVERT: L 243 MET cc_start: 0.2850 (mmm) cc_final: 0.1586 (ptp) REVERT: L 258 MET cc_start: -0.2933 (tmt) cc_final: -0.3439 (tmt) REVERT: L 272 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5032 (mt) REVERT: L 275 MET cc_start: -0.1262 (ttt) cc_final: -0.2029 (mtp) REVERT: L 305 LYS cc_start: 0.7446 (mmmm) cc_final: 0.7201 (mmmm) REVERT: L 581 LYS cc_start: 0.5692 (mtmm) cc_final: 0.3499 (mmmt) REVERT: L 587 GLU cc_start: 0.5788 (pt0) cc_final: 0.5339 (pt0) REVERT: M 54 LEU cc_start: 0.3441 (pt) cc_final: 0.1825 (mt) REVERT: M 69 MET cc_start: 0.6584 (ppp) cc_final: 0.6193 (mtt) REVERT: M 90 MET cc_start: 0.6432 (mmt) cc_final: 0.6179 (mmt) REVERT: M 118 LEU cc_start: 0.3417 (pp) cc_final: 0.1098 (tp) REVERT: M 185 MET cc_start: 0.4723 (ppp) cc_final: 0.4341 (ppp) REVERT: M 222 LEU cc_start: 0.7000 (mp) cc_final: 0.5680 (tp) REVERT: M 223 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.4898 (mt) REVERT: M 299 PHE cc_start: 0.5959 (m-10) cc_final: 0.5299 (m-10) REVERT: M 345 MET cc_start: 0.5481 (mmm) cc_final: 0.5270 (mmm) REVERT: M 466 PHE cc_start: 0.3323 (t80) cc_final: 0.2741 (t80) REVERT: N 25 MET cc_start: 0.6964 (ptp) cc_final: 0.6491 (tpt) REVERT: N 67 MET cc_start: 0.6068 (ttp) cc_final: 0.5174 (tmm) REVERT: N 74 MET cc_start: 0.2330 (mtp) cc_final: 0.1326 (mtt) REVERT: N 204 LEU cc_start: 0.6591 (pp) cc_final: 0.5992 (mp) REVERT: N 321 MET cc_start: 0.4201 (ptt) cc_final: 0.3998 (ptt) REVERT: N 359 LEU cc_start: 0.5605 (tt) cc_final: 0.5295 (tt) REVERT: N 379 MET cc_start: 0.6074 (tpp) cc_final: 0.5217 (tpp) REVERT: N 380 MET cc_start: 0.6555 (tmm) cc_final: 0.5802 (tmm) REVERT: N 397 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.6085 (m-10) REVERT: N 427 ARG cc_start: 0.7169 (mmp80) cc_final: 0.6507 (ttp80) outliers start: 144 outliers final: 118 residues processed: 1044 average time/residue: 0.4773 time to fit residues: 796.9336 Evaluate side-chains 1087 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 958 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR 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 261 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 862 TYR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 67 TRP Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 236 GLN Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 243 TRP Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 7.9990 chunk 421 optimal weight: 0.7980 chunk 384 optimal weight: 1.9990 chunk 409 optimal weight: 4.9990 chunk 420 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 321 optimal weight: 50.0000 chunk 125 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 387 optimal weight: 0.0980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 104 ASN ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS L 121 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36088 Z= 0.255 Angle : 0.716 13.951 49115 Z= 0.358 Chirality : 0.045 0.293 5554 Planarity : 0.005 0.058 6255 Dihedral : 5.651 171.909 4983 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 4.59 % Allowed : 25.88 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4573 helix: 0.77 (0.11), residues: 2478 sheet: -0.32 (0.29), residues: 309 loop : -1.11 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP M 122 HIS 0.015 0.001 HIS M 117 PHE 0.029 0.002 PHE M 480 TYR 0.040 0.002 TYR N 308 ARG 0.015 0.001 ARG G 214 *********************** 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 1127 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 965 time to evaluate : 3.988 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: A 116 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.4124 (t80) REVERT: B 170 MET cc_start: 0.7520 (mtp) cc_final: 0.6749 (mtp) REVERT: D 95 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7286 (p90) REVERT: D 106 ASP cc_start: 0.7204 (m-30) cc_final: 0.6816 (m-30) REVERT: D 139 ASP cc_start: 0.7732 (t0) cc_final: 0.7467 (t0) REVERT: D 228 ARG cc_start: 0.6240 (mtp85) cc_final: 0.5951 (mtp85) REVERT: D 290 LEU cc_start: 0.8842 (mt) cc_final: 0.8635 (mt) REVERT: D 385 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6639 (mmtm) REVERT: D 414 GLU cc_start: 0.6437 (mp0) cc_final: 0.6157 (tp30) REVERT: D 436 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7281 (mtmt) REVERT: D 483 ASN cc_start: 0.7100 (t0) cc_final: 0.6423 (t0) REVERT: E 31 ASP cc_start: 0.7527 (t0) cc_final: 0.5575 (m-30) REVERT: F 11 HIS cc_start: 0.8365 (m90) cc_final: 0.8043 (m-70) REVERT: F 15 TRP cc_start: 0.7765 (p-90) cc_final: 0.4504 (t60) REVERT: F 36 GLU cc_start: 0.7514 (mp0) cc_final: 0.7263 (pm20) REVERT: F 53 GLN cc_start: 0.8138 (mt0) cc_final: 0.6990 (tp-100) REVERT: F 71 LEU cc_start: 0.8505 (tt) cc_final: 0.8248 (tp) REVERT: F 94 MET cc_start: 0.7789 (tpp) cc_final: 0.7303 (tpt) REVERT: F 212 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8078 (mmtm) REVERT: F 220 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: F 237 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6454 (pp30) REVERT: F 252 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6138 (t80) REVERT: F 262 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.7083 (m-90) REVERT: F 299 PHE cc_start: 0.7760 (m-80) cc_final: 0.7492 (m-80) REVERT: G 108 GLU cc_start: 0.6988 (tt0) cc_final: 0.6737 (tt0) REVERT: G 260 TYR cc_start: 0.8344 (m-80) cc_final: 0.7867 (m-80) REVERT: G 326 PHE cc_start: 0.7457 (t80) cc_final: 0.7015 (t80) REVERT: G 408 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7490 (tp-100) REVERT: G 414 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: G 420 ASN cc_start: 0.7424 (t0) cc_final: 0.7159 (t0) REVERT: G 447 TYR cc_start: 0.7936 (t80) cc_final: 0.7721 (t80) REVERT: G 453 ASP cc_start: 0.7452 (m-30) cc_final: 0.7205 (m-30) REVERT: G 454 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6821 (mm-40) REVERT: G 495 LYS cc_start: 0.7951 (mttt) cc_final: 0.7464 (mtmm) REVERT: G 570 ASP cc_start: 0.8053 (t0) cc_final: 0.7696 (p0) REVERT: G 634 TYR cc_start: 0.8544 (p90) cc_final: 0.8283 (p90) REVERT: G 644 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6660 (t) REVERT: G 734 PHE cc_start: 0.6967 (m-80) cc_final: 0.6672 (m-80) REVERT: G 742 ASN cc_start: 0.8490 (t0) cc_final: 0.8224 (t0) REVERT: G 767 LYS cc_start: 0.8447 (mppt) cc_final: 0.8154 (mppt) REVERT: G 769 GLN cc_start: 0.6540 (mm-40) cc_final: 0.6078 (mm-40) REVERT: G 838 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8485 (Cg_endo) REVERT: G 842 LEU cc_start: 0.8077 (mt) cc_final: 0.7780 (mt) REVERT: H 131 LEU cc_start: 0.7934 (mt) cc_final: 0.7376 (mt) REVERT: H 236 LEU cc_start: 0.5792 (mp) cc_final: 0.5118 (tp) REVERT: H 245 ILE cc_start: 0.4230 (tp) cc_final: 0.3954 (tp) REVERT: H 267 PRO cc_start: 0.7536 (Cg_endo) cc_final: 0.7298 (Cg_exo) REVERT: H 298 MET cc_start: 0.4729 (ptp) cc_final: 0.3751 (ppp) REVERT: I 53 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6315 (t0) REVERT: J 74 LEU cc_start: 0.8567 (mt) cc_final: 0.8245 (tt) REVERT: K 25 ARG cc_start: 0.6806 (tpm170) cc_final: 0.6265 (tpm170) REVERT: K 31 MET cc_start: 0.6196 (mpp) cc_final: 0.5624 (tpp) REVERT: K 98 MET cc_start: 0.1988 (mtm) cc_final: 0.1387 (mtm) REVERT: L 1 MET cc_start: 0.1568 (ptt) cc_final: -0.1122 (ppp) REVERT: L 122 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5187 (mt) REVERT: L 243 MET cc_start: 0.2428 (mmm) cc_final: 0.1279 (ptp) REVERT: L 258 MET cc_start: -0.2808 (tmt) cc_final: -0.3365 (tmt) REVERT: L 275 MET cc_start: -0.1338 (ttt) cc_final: -0.2088 (mtp) REVERT: L 305 LYS cc_start: 0.7250 (mmmm) cc_final: 0.6994 (mmmm) REVERT: L 581 LYS cc_start: 0.5949 (mtmm) cc_final: 0.3954 (mmmt) REVERT: L 587 GLU cc_start: 0.5922 (pt0) cc_final: 0.5494 (pt0) REVERT: L 610 MET cc_start: 0.3648 (tpt) cc_final: 0.3410 (tpt) REVERT: M 54 LEU cc_start: 0.3712 (pt) cc_final: 0.2141 (mt) REVERT: M 69 MET cc_start: 0.6347 (ppp) cc_final: 0.6110 (mtt) REVERT: M 90 MET cc_start: 0.6423 (mmt) cc_final: 0.6039 (mmt) REVERT: M 131 PHE cc_start: 0.5756 (m-10) cc_final: 0.5397 (m-10) REVERT: M 185 MET cc_start: 0.4703 (ppp) cc_final: 0.4344 (ppp) REVERT: M 222 LEU cc_start: 0.7387 (mp) cc_final: 0.6690 (mp) REVERT: M 223 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.4880 (mt) REVERT: M 299 PHE cc_start: 0.5850 (m-10) cc_final: 0.5326 (m-10) REVERT: M 345 MET cc_start: 0.5482 (mmm) cc_final: 0.5260 (mmm) REVERT: M 366 ILE cc_start: 0.3676 (pt) cc_final: 0.2449 (mt) REVERT: M 374 MET cc_start: 0.1229 (ttt) cc_final: 0.0064 (mtm) REVERT: M 409 MET cc_start: 0.4793 (ppp) cc_final: 0.4491 (ppp) REVERT: N 67 MET cc_start: 0.6001 (ttp) cc_final: 0.4784 (tmm) REVERT: N 74 MET cc_start: 0.2266 (mtp) cc_final: 0.1644 (mtt) REVERT: N 176 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6333 (tt) REVERT: N 204 LEU cc_start: 0.6612 (pp) cc_final: 0.6019 (mp) REVERT: N 260 TYR cc_start: 0.6805 (m-10) cc_final: 0.5829 (m-80) REVERT: N 287 MET cc_start: 0.4329 (tmm) cc_final: 0.3721 (tmm) REVERT: N 359 LEU cc_start: 0.5403 (tt) cc_final: 0.5006 (tt) REVERT: N 379 MET cc_start: 0.6295 (tpp) cc_final: 0.5450 (tpp) REVERT: N 380 MET cc_start: 0.6566 (tmm) cc_final: 0.5775 (tmm) REVERT: N 397 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: N 408 TRP cc_start: 0.7457 (OUTLIER) cc_final: 0.7076 (m-90) REVERT: N 427 ARG cc_start: 0.7231 (mmp80) cc_final: 0.6579 (ttp80) outliers start: 162 outliers final: 129 residues processed: 1047 average time/residue: 0.4862 time to fit residues: 820.1442 Evaluate side-chains 1090 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 946 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 220 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 261 LEU Chi-restraints excluded: chain F residue 262 TRP Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 862 TYR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain G residue 889 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 67 TRP Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 243 TRP Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 123 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 404 GLN Chi-restraints excluded: chain N residue 408 TRP Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 5.9990 chunk 268 optimal weight: 0.1980 chunk 433 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 205 optimal weight: 0.2980 chunk 301 optimal weight: 6.9990 chunk 454 optimal weight: 4.9990 chunk 418 optimal weight: 1.9990 chunk 361 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 chunk 279 optimal weight: 2.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 123 ASN ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36088 Z= 0.191 Angle : 0.718 16.293 49115 Z= 0.356 Chirality : 0.044 0.353 5554 Planarity : 0.005 0.072 6255 Dihedral : 5.490 170.146 4983 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.88 % Allowed : 26.76 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4573 helix: 0.86 (0.11), residues: 2475 sheet: -0.33 (0.28), residues: 327 loop : -1.02 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP L 217 HIS 0.012 0.001 HIS G 259 PHE 0.032 0.002 PHE L 53 TYR 0.037 0.002 TYR N 308 ARG 0.014 0.001 ARG G 214 ********************** 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 1108 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 971 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ASN cc_start: 0.6727 (m110) cc_final: 0.6217 (p0) REVERT: B 59 PHE cc_start: 0.7185 (t80) cc_final: 0.6769 (t80) REVERT: D 95 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7155 (p90) REVERT: D 106 ASP cc_start: 0.7025 (m-30) cc_final: 0.6691 (m-30) REVERT: D 139 ASP cc_start: 0.7456 (t0) cc_final: 0.7157 (t0) REVERT: D 158 GLN cc_start: 0.7181 (mm110) cc_final: 0.6939 (mm110) REVERT: D 228 ARG cc_start: 0.6141 (mtp85) cc_final: 0.5885 (mtp85) REVERT: D 283 TYR cc_start: 0.8478 (t80) cc_final: 0.8208 (t80) REVERT: D 290 LEU cc_start: 0.8702 (mt) cc_final: 0.8183 (tp) REVERT: D 385 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6587 (mmtm) REVERT: D 436 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6790 (mtmt) REVERT: D 483 ASN cc_start: 0.7019 (t0) cc_final: 0.6357 (t0) REVERT: D 532 MET cc_start: 0.7104 (mmm) cc_final: 0.6844 (mmp) REVERT: F 36 GLU cc_start: 0.7382 (mp0) cc_final: 0.6966 (pm20) REVERT: F 49 GLU cc_start: 0.7207 (pt0) cc_final: 0.6795 (pt0) REVERT: F 53 GLN cc_start: 0.8005 (mt0) cc_final: 0.6888 (tp-100) REVERT: F 71 LEU cc_start: 0.8411 (tt) cc_final: 0.8171 (tp) REVERT: F 94 MET cc_start: 0.8101 (tpp) cc_final: 0.7166 (tpt) REVERT: F 220 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: F 237 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6297 (pp30) REVERT: F 252 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6462 (t80) REVERT: F 262 TRP cc_start: 0.7953 (OUTLIER) cc_final: 0.6932 (m-90) REVERT: F 299 PHE cc_start: 0.7733 (m-80) cc_final: 0.7413 (m-80) REVERT: G 326 PHE cc_start: 0.7392 (t80) cc_final: 0.6669 (t80) REVERT: G 402 ARG cc_start: 0.6712 (mtm180) cc_final: 0.6480 (mtm180) REVERT: G 408 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7421 (tp-100) REVERT: G 432 THR cc_start: 0.7596 (m) cc_final: 0.6930 (p) REVERT: G 440 ASP cc_start: 0.6507 (m-30) cc_final: 0.6179 (m-30) REVERT: G 447 TYR cc_start: 0.7827 (t80) cc_final: 0.7597 (t80) REVERT: G 453 ASP cc_start: 0.7202 (m-30) cc_final: 0.6921 (m-30) REVERT: G 495 LYS cc_start: 0.7802 (mttt) cc_final: 0.7347 (mtmm) REVERT: G 551 GLU cc_start: 0.6659 (mp0) cc_final: 0.6108 (mp0) REVERT: G 570 ASP cc_start: 0.7998 (t0) cc_final: 0.7678 (p0) REVERT: G 629 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5487 (tpp80) REVERT: G 644 VAL cc_start: 0.7081 (OUTLIER) cc_final: 0.6554 (t) REVERT: G 842 LEU cc_start: 0.8235 (mt) cc_final: 0.7994 (mt) REVERT: H 131 LEU cc_start: 0.7840 (mt) cc_final: 0.7373 (mt) REVERT: H 236 LEU cc_start: 0.5617 (mp) cc_final: 0.5024 (tp) REVERT: H 267 PRO cc_start: 0.7585 (Cg_endo) cc_final: 0.7355 (Cg_exo) REVERT: H 298 MET cc_start: 0.4692 (ptp) cc_final: 0.3754 (ppp) REVERT: J 74 LEU cc_start: 0.8537 (mt) cc_final: 0.8254 (tt) REVERT: K 25 ARG cc_start: 0.6800 (tpm170) cc_final: 0.6386 (tpm170) REVERT: K 31 MET cc_start: 0.5990 (mpp) cc_final: 0.5506 (tpp) REVERT: K 98 MET cc_start: 0.1970 (mtm) cc_final: 0.1388 (mtm) REVERT: L 1 MET cc_start: 0.1677 (ptt) cc_final: -0.1061 (ppp) REVERT: L 122 LEU cc_start: 0.4656 (OUTLIER) cc_final: 0.3803 (mt) REVERT: L 243 MET cc_start: 0.2347 (mmm) cc_final: 0.1164 (ptp) REVERT: L 258 MET cc_start: -0.3114 (tmt) cc_final: -0.3525 (tmt) REVERT: L 275 MET cc_start: -0.1571 (ttt) cc_final: -0.2221 (mtp) REVERT: L 305 LYS cc_start: 0.7295 (mmmm) cc_final: 0.7032 (mmmm) REVERT: L 581 LYS cc_start: 0.5903 (mtmm) cc_final: 0.3898 (mmmt) REVERT: L 610 MET cc_start: 0.3464 (tpt) cc_final: 0.3258 (tpt) REVERT: M 15 PHE cc_start: 0.5272 (m-80) cc_final: 0.4927 (m-10) REVERT: M 54 LEU cc_start: 0.3595 (pt) cc_final: 0.2086 (mt) REVERT: M 69 MET cc_start: 0.6293 (ppp) cc_final: 0.6081 (mtt) REVERT: M 90 MET cc_start: 0.6408 (mmt) cc_final: 0.5927 (mmt) REVERT: M 222 LEU cc_start: 0.7332 (mp) cc_final: 0.6095 (tp) REVERT: M 223 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.4754 (mt) REVERT: M 299 PHE cc_start: 0.6010 (m-10) cc_final: 0.5441 (m-10) REVERT: M 345 MET cc_start: 0.5470 (mmm) cc_final: 0.5237 (mmm) REVERT: M 361 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.5399 (tp-100) REVERT: N 52 LEU cc_start: 0.6073 (tt) cc_final: 0.5864 (mt) REVERT: N 67 MET cc_start: 0.6039 (ttp) cc_final: 0.4846 (tmm) REVERT: N 74 MET cc_start: 0.1986 (mtp) cc_final: 0.1519 (mtt) REVERT: N 121 ASN cc_start: 0.2355 (OUTLIER) cc_final: 0.1997 (m-40) REVERT: N 123 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6570 (t0) REVERT: N 204 LEU cc_start: 0.6587 (pp) cc_final: 0.6023 (mp) REVERT: N 359 LEU cc_start: 0.5328 (tt) cc_final: 0.5019 (tt) REVERT: N 379 MET cc_start: 0.6145 (tpp) cc_final: 0.5332 (tpp) REVERT: N 380 MET cc_start: 0.6535 (tmm) cc_final: 0.5817 (tmm) REVERT: N 397 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.6071 (m-10) REVERT: N 427 ARG cc_start: 0.6828 (mmp80) cc_final: 0.6562 (ttp80) outliers start: 137 outliers final: 107 residues processed: 1035 average time/residue: 0.4828 time to fit residues: 799.1076 Evaluate side-chains 1054 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 934 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 220 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 261 LEU Chi-restraints excluded: chain F residue 262 TRP Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 581 ASN Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 705 GLU Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain G residue 760 ASN Chi-restraints excluded: chain G residue 825 SER Chi-restraints excluded: chain G residue 862 TYR Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 187 TRP Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 67 TRP Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 273 PHE Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 223 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 243 TRP Chi-restraints excluded: chain M residue 361 GLN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 123 ASN Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 360 PHE Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 385 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 362 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 372 optimal weight: 8.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 HIS ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 ASN ** G 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.242636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.203253 restraints weight = 60516.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.206052 restraints weight = 78659.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.206948 restraints weight = 38125.089| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36088 Z= 0.209 Angle : 0.720 14.356 49115 Z= 0.357 Chirality : 0.044 0.351 5554 Planarity : 0.005 0.059 6255 Dihedral : 5.468 170.623 4983 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.94 % Allowed : 26.79 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 4573 helix: 0.88 (0.11), residues: 2472 sheet: -0.11 (0.30), residues: 305 loop : -1.01 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP L 143 HIS 0.011 0.001 HIS M 322 PHE 0.034 0.002 PHE D 489 TYR 0.038 0.002 TYR N 308 ARG 0.013 0.001 ARG G 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12183.25 seconds wall clock time: 216 minutes 16.41 seconds (12976.41 seconds total)