Starting phenix.real_space_refine on Mon Apr 15 16:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyv_12655/04_2024/7nyv_12655_updated.pdb" } resolution = 3.7 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 "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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35228 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1222 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4725 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'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: "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: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 668 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1985 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'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: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 21, 'TRANS': 482} Chain: "L" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4126 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 18, 'TRANS': 593} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'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: "N" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3543 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 810 SG CYS B 158 176.673 109.535 71.531 1.00 70.15 S ATOM 181 SG CYS B 64 174.302 103.600 71.206 1.00 92.83 S ATOM 175 SG CYS B 63 171.053 106.727 68.030 1.00 97.83 S ATOM 593 SG CYS B 129 171.469 109.724 73.377 1.00 67.58 S ATOM 6594 SG CYS E 92 224.613 164.830 67.842 1.00 62.87 S ATOM 6628 SG CYS E 97 227.316 164.614 66.047 1.00 69.61 S ATOM 6907 SG CYS E 133 221.704 168.480 66.062 1.00 63.52 S ATOM 6933 SG CYS E 137 223.508 169.129 64.342 1.00 67.90 S ATOM 9934 SG CYS F 357 204.884 159.479 67.080 1.00 47.47 S ATOM 9914 SG CYS F 354 200.223 159.714 68.042 1.00 48.35 S ATOM 10255 SG CYS F 398 202.825 165.207 66.923 1.00 45.59 S ATOM 9890 SG CYS F 351 203.245 162.718 72.597 1.00 47.04 S ATOM 10951 SG CYS G 48 187.375 157.819 67.040 1.00 45.65 S ATOM 11100 SG CYS G 67 187.745 160.399 69.592 1.00 43.17 S ATOM 10849 SG CYS G 34 189.980 158.082 72.639 1.00 49.82 S ATOM 10925 SG CYS G 45 190.966 155.233 70.663 1.00 45.41 S ATOM 11831 SG CYS G 157 195.183 154.643 83.799 1.00 40.35 S ATOM 11783 SG CYS G 151 198.488 151.005 79.916 1.00 44.33 S ATOM 11802 SG CYS G 154 192.578 153.093 78.372 1.00 49.00 S ATOM 12179 SG CYS G 201 192.507 148.908 82.598 1.00 39.75 S ATOM 11408 SG CYS G 106 193.241 139.839 81.848 1.00 40.86 S ATOM 11388 SG CYS G 103 194.041 137.198 75.907 1.00 57.52 S ATOM 11448 SG CYS G 112 190.243 142.676 77.499 1.00 40.82 S ATOM 12428 SG CYS G 231 174.947 154.632 100.969 1.00 49.12 S ATOM 12452 SG CYS G 235 175.487 153.642 95.435 1.00 42.65 S ATOM 12689 SG CYS G 263 179.308 152.819 97.857 1.00 57.31 S ATOM 12404 SG CYS G 228 175.598 150.092 98.316 1.00 45.04 S ATOM 12452 SG CYS G 235 175.487 153.642 95.435 1.00 42.65 S ATOM 12404 SG CYS G 228 175.598 150.092 98.316 1.00 45.04 S ATOM 12689 SG CYS G 263 179.308 152.819 97.857 1.00 57.31 S ATOM 18292 SG CYS I 109 193.129 123.215 77.714 1.00 48.64 S ATOM 17915 SG CYS I 60 192.783 123.131 84.331 1.00 48.98 S ATOM 17955 SG CYS I 66 187.647 122.689 80.597 1.00 46.59 S ATOM 17933 SG CYS I 63 190.911 127.536 79.690 1.00 48.39 S ATOM 17978 SG CYS I 70 180.389 119.358 77.416 1.00 52.21 S ATOM 18245 SG CYS I 102 181.972 117.249 72.525 1.00 53.20 S ATOM 18220 SG CYS I 99 182.436 112.975 77.592 1.00 59.90 S ATOM 18263 SG CYS I 105 186.401 117.868 75.896 1.00 56.35 S Time building chain proxies: 18.01, per 1000 atoms: 0.51 Number of scatterers: 35228 At special positions: 0 Unit cell: (254.43, 214.338, 143.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 243 16.00 P 1 15.00 O 6270 8.00 N 5962 7.00 C 22719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 13.77 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " Number of angles added : 93 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 21 sheets defined 52.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.747A 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 62 removed outlier: 3.590A pdb=" N LEU D 53 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 140 removed outlier: 4.033A pdb=" N TRP D 132 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.969A 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: 4.243A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.784A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.776A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 4.114A 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 332 through 349 removed outlier: 3.981A 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: 3.904A pdb=" N ILE D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Proline residue: D 569 - end of helix Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.980A pdb=" N HIS E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.492A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 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: 3.803A 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: 4.051A pdb=" N ASN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.758A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 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: 4.800A 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 162 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 removed outlier: 3.640A pdb=" N GLU G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) No H-bonds generated for '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: 3.696A pdb=" N GLY G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS G 400 " --> pdb=" O ALA G 396 " (cutoff:3.500A) removed outlier: 5.082A 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 585 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 688 removed outlier: 5.222A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 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 '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 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' 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: 4.051A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 58 removed outlier: 4.096A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 90 through 113 removed outlier: 3.714A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.859A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.708A 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 'A' and resid 16 through 37 Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.726A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.479A 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 'H' and resid 57 through 67 Processing helix chain 'H' and resid 81 through 100 Proline residue: H 87 - end of helix removed outlier: 3.665A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 137 removed outlier: 4.359A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 156 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.041A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 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 305 through 320 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: 4.317A 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: 4.272A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 removed outlier: 3.532A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU M 355 " --> pdb=" O SER M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 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: 4.822A 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: 3.719A pdb=" N LEU M 471 " --> pdb=" O MET M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 483 through 502 removed outlier: 5.120A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 removed outlier: 4.231A 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: 4.013A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 removed outlier: 3.677A pdb=" N VAL L 92 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 132 removed outlier: 3.802A 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: 3.931A pdb=" N ALA L 167 " --> pdb=" O ASN L 163 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA L 184 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 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: 3.684A 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: 3.565A 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: 3.885A 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: 4.079A pdb=" N PHE L 340 " --> pdb=" O MET L 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 344 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) 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: 3.847A pdb=" N ARG L 431 " --> pdb=" O LEU L 427 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 464 Proline residue: L 456 - end of helix Processing helix chain 'L' and resid 466 through 470 removed outlier: 3.548A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 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 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 removed outlier: 3.591A 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: 3.576A pdb=" N PHE N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 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: 3.971A pdb=" N HIS N 224 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 5.723A 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: 4.844A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.934A 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: 3.697A pdb=" N PHE N 258 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 285 removed outlier: 3.887A pdb=" N VAL N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 315 removed outlier: 3.826A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 4.304A 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: 4.654A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR N 425 " --> pdb=" O GLY N 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) removed outlier: 4.754A 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 59 removed outlier: 6.739A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.438A 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: 6.650A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 119 through 121 removed outlier: 7.063A 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: 4.114A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing sheet with id= 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: 6.640A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 86 through 91 removed outlier: 6.807A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.242A 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 9 through 13 removed outlier: 6.717A pdb=" N THR G 75 " --> pdb=" O HIS G 5 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 144 through 146 Processing sheet with id= K, first strand: chain 'G' and resid 171 through 173 Processing sheet with id= L, first strand: chain 'G' and resid 222 through 227 removed outlier: 3.642A pdb=" N ALA G 224 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG G 248 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG G 242 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'G' and resid 312 through 315 removed outlier: 6.607A pdb=" N ALA G 563 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE G 315 " --> pdb=" O ALA G 563 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU G 589 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL G 566 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU G 606 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP G 594 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU G 608 " --> pdb=" O ASP G 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 445 through 448 removed outlier: 6.938A pdb=" N VAL G 375 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR G 432 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 377 " --> pdb=" O THR G 432 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY G 501 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY G 528 " --> pdb=" O ILE G 498 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 500 " --> pdb=" O GLY G 528 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N THR G 530 " --> pdb=" O SER G 500 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 618 through 621 Processing sheet with id= Q, first strand: chain 'G' and resid 811 through 815 removed outlier: 7.409A pdb=" N TYR G 839 " --> pdb=" O PRO G 885 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE G 840 " --> pdb=" O THR G 868 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU G 842 " --> pdb=" O PRO G 870 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU G 872 " --> pdb=" O LEU G 842 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 47 through 50 Processing sheet with id= S, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.700A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= U, first strand: chain 'L' and resid 66 through 70 removed outlier: 7.213A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) 1638 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: 12.42 Time building geometry restraints manager: 14.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 15233 1.43 - 1.65: 20397 1.65 - 1.86: 366 1.86 - 2.07: 0 2.07 - 2.29: 92 Bond restraints: 36088 Sorted by residual: bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" CB CSX E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CB CSX B 102 " pdb=" SG CSX B 102 " ideal model delta sigma weight residual 1.831 1.761 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.30e-02 5.92e+03 6.01e+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 3.39e+00 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 73.32 - 85.47: 88 85.47 - 97.62: 2 97.62 - 109.78: 5294 109.78 - 121.93: 36917 121.93 - 134.09: 6814 Bond angle restraints: 49115 Sorted by residual: angle pdb=" N CYS B 64 " pdb=" CA CYS B 64 " pdb=" CB CYS B 64 " ideal model delta sigma weight residual 114.17 109.07 5.10 1.14e+00 7.69e-01 2.00e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.50 4.87 1.34e+00 5.57e-01 1.32e+01 angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA CYS G 228 " pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " ideal model delta sigma weight residual 114.40 122.67 -8.27 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N VAL N 221 " pdb=" CA VAL N 221 " pdb=" C VAL N 221 " ideal model delta sigma weight residual 108.88 115.92 -7.04 2.16e+00 2.14e-01 1.06e+01 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 20679 34.05 - 68.09: 395 68.09 - 102.14: 28 102.14 - 136.19: 0 136.19 - 170.24: 1 Dihedral angle restraints: 21103 sinusoidal: 7915 harmonic: 13188 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.36 170.24 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 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL K 23 " pdb=" C VAL K 23 " pdb=" N ILE K 24 " pdb=" CA ILE K 24 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 21100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4330 0.053 - 0.105: 1027 0.105 - 0.158: 178 0.158 - 0.211: 16 0.211 - 0.264: 3 Chirality restraints: 5554 Sorted by residual: chirality pdb=" CA PHE L 341 " pdb=" N PHE L 341 " pdb=" C PHE L 341 " pdb=" CB PHE L 341 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL L 35 " pdb=" CA VAL L 35 " pdb=" CG1 VAL L 35 " pdb=" CG2 VAL L 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU L 299 " pdb=" CB LEU L 299 " pdb=" CD1 LEU L 299 " pdb=" CD2 LEU L 299 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5551 not shown) Planarity restraints: 6255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 356 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C PRO F 356 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO F 356 " 0.026 2.00e-02 2.50e+03 pdb=" N CYS F 357 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU G 457 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU G 457 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY G 458 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 30 " 0.031 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP M 30 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 30 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP M 30 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 30 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 30 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 30 " 0.004 2.00e-02 2.50e+03 ... (remaining 6252 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 147 2.51 - 3.11: 25830 3.11 - 3.71: 56288 3.71 - 4.30: 77966 4.30 - 4.90: 130053 Nonbonded interactions: 290284 Sorted by model distance: nonbonded pdb=" OG SER K 67 " pdb=" OH TYR A 84 " model vdw 1.913 2.440 nonbonded pdb=" OE1 GLN G 632 " pdb="CA CA G1005 " model vdw 2.179 2.510 nonbonded pdb=" OE2 GLU G 624 " pdb=" NH2 ARG G 784 " model vdw 2.213 2.520 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.218 2.520 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.222 2.440 ... (remaining 290279 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: 0.880 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: 5.380 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 96.950 Find NCS groups from input model: 1.270 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36088 Z= 0.328 Angle : 0.846 8.530 49115 Z= 0.447 Chirality : 0.046 0.264 5554 Planarity : 0.006 0.082 6255 Dihedral : 13.962 170.237 12663 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.85 % Allowed : 2.78 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.11), residues: 4573 helix: -0.92 (0.09), residues: 2476 sheet: -0.39 (0.30), residues: 299 loop : -1.33 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP M 30 HIS 0.012 0.001 HIS F 400 PHE 0.046 0.003 PHE N 396 TYR 0.054 0.002 TYR N 397 ARG 0.014 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 1495 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1465 time to evaluate : 4.127 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: B 57 TYR cc_start: 0.7037 (t80) cc_final: 0.6607 (t80) REVERT: B 103 PHE cc_start: 0.6145 (m-80) cc_final: 0.4868 (m-80) REVERT: B 106 MET cc_start: 0.6777 (ppp) cc_final: 0.6352 (ppp) REVERT: B 113 LEU cc_start: 0.8543 (mp) cc_final: 0.8220 (mt) REVERT: B 146 ASP cc_start: 0.7977 (p0) cc_final: 0.7652 (t0) REVERT: D 18 ASP cc_start: 0.7750 (p0) cc_final: 0.7481 (p0) REVERT: D 77 ASP cc_start: 0.7073 (t70) cc_final: 0.6673 (t70) REVERT: D 91 ASP cc_start: 0.6876 (m-30) cc_final: 0.5992 (t0) REVERT: D 110 LYS cc_start: 0.7900 (mttp) cc_final: 0.7568 (mtpp) REVERT: D 294 THR cc_start: 0.8191 (m) cc_final: 0.7820 (p) REVERT: D 496 THR cc_start: 0.8488 (m) cc_final: 0.8252 (m) REVERT: D 553 TYR cc_start: 0.7832 (t80) cc_final: 0.7628 (t80) REVERT: D 555 THR cc_start: 0.8417 (m) cc_final: 0.8206 (p) REVERT: E 45 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8185 (tptp) REVERT: E 142 ASN cc_start: 0.7445 (m-40) cc_final: 0.7228 (m-40) REVERT: F 33 ASN cc_start: 0.8331 (t0) cc_final: 0.7755 (t0) REVERT: F 186 LEU cc_start: 0.9293 (tt) cc_final: 0.9088 (tt) REVERT: G 21 GLU cc_start: 0.7914 (pt0) cc_final: 0.7565 (pt0) REVERT: G 55 ASN cc_start: 0.7398 (p0) cc_final: 0.7181 (p0) REVERT: G 78 SER cc_start: 0.8882 (t) cc_final: 0.8399 (p) REVERT: G 111 ASN cc_start: 0.7767 (t0) cc_final: 0.7275 (t0) REVERT: G 137 ASN cc_start: 0.8227 (m-40) cc_final: 0.7385 (m110) REVERT: G 147 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6633 (mm-30) REVERT: G 173 TYR cc_start: 0.8433 (m-80) cc_final: 0.7691 (m-80) REVERT: G 311 LYS cc_start: 0.7702 (tttt) cc_final: 0.7161 (tttp) REVERT: G 497 LEU cc_start: 0.8731 (tp) cc_final: 0.8490 (tp) REVERT: G 537 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7171 (t0) REVERT: G 539 MET cc_start: 0.6546 (mmt) cc_final: 0.6291 (mmm) REVERT: G 548 SER cc_start: 0.5870 (p) cc_final: 0.4891 (t) REVERT: G 589 LEU cc_start: 0.7814 (tp) cc_final: 0.7279 (mm) REVERT: G 653 HIS cc_start: 0.6335 (t-90) cc_final: 0.5695 (t-170) REVERT: G 663 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7465 (mm-30) REVERT: G 665 ASP cc_start: 0.6118 (t0) cc_final: 0.5756 (p0) REVERT: G 671 HIS cc_start: 0.6622 (m170) cc_final: 0.5967 (t-90) REVERT: G 772 VAL cc_start: 0.8491 (p) cc_final: 0.7595 (p) REVERT: G 804 GLN cc_start: 0.7280 (tp40) cc_final: 0.6890 (tm-30) REVERT: G 810 TRP cc_start: 0.7301 (m100) cc_final: 0.7055 (m100) REVERT: G 905 GLU cc_start: 0.4938 (mp0) cc_final: 0.3488 (mp0) REVERT: I 78 GLN cc_start: 0.8099 (tp40) cc_final: 0.7846 (tp40) REVERT: I 106 GLU cc_start: 0.7412 (tt0) cc_final: 0.7098 (tt0) REVERT: I 126 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7314 (tptp) REVERT: I 162 ASP cc_start: 0.5712 (t70) cc_final: 0.5118 (t70) REVERT: K 39 ILE cc_start: 0.5900 (mt) cc_final: 0.5075 (mt) REVERT: K 98 MET cc_start: 0.5827 (ptt) cc_final: 0.5355 (ppp) REVERT: J 1 MET cc_start: 0.2903 (tpt) cc_final: 0.2694 (tmm) REVERT: J 33 ILE cc_start: 0.6609 (mm) cc_final: 0.6323 (mm) REVERT: J 112 LEU cc_start: 0.6216 (pp) cc_final: 0.5851 (mt) REVERT: H 88 MET cc_start: 0.5745 (mpp) cc_final: 0.4598 (mtp) REVERT: H 237 PHE cc_start: 0.6026 (m-10) cc_final: 0.5420 (t80) REVERT: M 63 TRP cc_start: 0.3370 (m-90) cc_final: 0.2392 (m-10) REVERT: M 336 LEU cc_start: 0.8522 (tp) cc_final: 0.6590 (pt) REVERT: M 418 VAL cc_start: 0.6863 (p) cc_final: 0.6600 (m) REVERT: M 467 MET cc_start: 0.7724 (ptt) cc_final: 0.7268 (mtp) REVERT: M 486 LEU cc_start: 0.7241 (mt) cc_final: 0.6680 (mt) REVERT: L 158 TYR cc_start: 0.5226 (p90) cc_final: 0.4079 (p90) REVERT: L 159 THR cc_start: 0.8109 (p) cc_final: 0.7784 (p) REVERT: L 191 GLU cc_start: 0.6007 (tp30) cc_final: 0.5637 (tp30) REVERT: L 203 LEU cc_start: 0.8131 (tt) cc_final: 0.6531 (mp) REVERT: L 212 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6344 (p0) REVERT: L 246 PRO cc_start: 0.4701 (Cg_exo) cc_final: 0.4499 (Cg_endo) REVERT: L 270 HIS cc_start: 0.7885 (p-80) cc_final: 0.7487 (p-80) REVERT: L 275 MET cc_start: 0.3948 (mmm) cc_final: 0.3695 (mmt) REVERT: L 347 LEU cc_start: -0.3654 (mt) cc_final: -0.4286 (pp) REVERT: L 574 VAL cc_start: 0.4241 (t) cc_final: 0.4020 (p) REVERT: L 592 ARG cc_start: 0.5481 (mtt90) cc_final: 0.4230 (ptt90) REVERT: N 8 LEU cc_start: 0.6462 (mt) cc_final: 0.5600 (pp) REVERT: N 61 MET cc_start: 0.3279 (ppp) cc_final: 0.2702 (ptt) REVERT: N 74 MET cc_start: 0.4448 (mtp) cc_final: 0.4199 (mmm) REVERT: N 203 LEU cc_start: 0.5885 (tp) cc_final: 0.5582 (mt) REVERT: N 379 MET cc_start: 0.5711 (mmt) cc_final: 0.5121 (mmt) REVERT: N 427 ARG cc_start: 0.6742 (mtm180) cc_final: 0.6438 (mmm160) outliers start: 30 outliers final: 8 residues processed: 1482 average time/residue: 0.5198 time to fit residues: 1215.2001 Evaluate side-chains 1091 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1081 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain N residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 357 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 414 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN B 196 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 279 ASN D 340 GLN D 517 GLN E 78 GLN E 100 ASN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 304 HIS F 400 HIS G 196 ASN G 229 GLN G 605 HIS G 766 ASN I 128 GLN K 40 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN L 100 HIS L 135 ASN L 232 GLN L 338 HIS N 46 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 36088 Z= 0.285 Angle : 0.711 12.101 49115 Z= 0.361 Chirality : 0.046 0.264 5554 Planarity : 0.006 0.078 6255 Dihedral : 5.805 169.564 5002 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 3.88 % Allowed : 14.06 % Favored : 82.06 % 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: -0.72 (0.12), residues: 4573 helix: 0.06 (0.10), residues: 2463 sheet: -0.17 (0.30), residues: 295 loop : -1.17 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 65 HIS 0.012 0.001 HIS N 305 PHE 0.034 0.002 PHE L 53 TYR 0.036 0.002 TYR L 189 ARG 0.012 0.001 ARG D 172 *********************** 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 1248 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1111 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 TYR cc_start: 0.7165 (t80) cc_final: 0.6671 (t80) REVERT: B 103 PHE cc_start: 0.6343 (m-80) cc_final: 0.5473 (m-80) REVERT: B 146 ASP cc_start: 0.8239 (p0) cc_final: 0.7885 (t0) REVERT: D 48 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7162 (pt) REVERT: D 60 LEU cc_start: 0.8408 (mp) cc_final: 0.8199 (mp) REVERT: D 110 LYS cc_start: 0.8013 (mttp) cc_final: 0.7638 (mtpp) REVERT: D 195 PHE cc_start: 0.6091 (p90) cc_final: 0.5382 (t80) REVERT: D 444 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: D 449 GLU cc_start: 0.5811 (pp20) cc_final: 0.5385 (pp20) REVERT: D 486 GLU cc_start: 0.7335 (pm20) cc_final: 0.7099 (pm20) REVERT: D 524 MET cc_start: 0.8366 (mmm) cc_final: 0.8033 (mmm) REVERT: D 541 SER cc_start: 0.6661 (p) cc_final: 0.6359 (t) REVERT: D 542 TYR cc_start: 0.6617 (m-80) cc_final: 0.6117 (m-80) REVERT: D 553 TYR cc_start: 0.8058 (t80) cc_final: 0.7643 (t80) REVERT: D 555 THR cc_start: 0.8669 (m) cc_final: 0.8460 (p) REVERT: E 18 GLU cc_start: 0.8005 (mp0) cc_final: 0.7541 (mp0) REVERT: E 45 LYS cc_start: 0.8494 (tmmt) cc_final: 0.8080 (tptp) REVERT: E 90 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7327 (mtm-85) REVERT: F 36 GLU cc_start: 0.4174 (pm20) cc_final: 0.3587 (pm20) REVERT: F 94 MET cc_start: 0.6852 (tpp) cc_final: 0.6495 (ttm) REVERT: F 101 ASP cc_start: 0.7835 (m-30) cc_final: 0.6917 (m-30) REVERT: F 219 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7239 (m) REVERT: G 21 GLU cc_start: 0.8292 (pt0) cc_final: 0.7816 (pt0) REVERT: G 78 SER cc_start: 0.8926 (t) cc_final: 0.8407 (p) REVERT: G 111 ASN cc_start: 0.7887 (t0) cc_final: 0.7519 (t0) REVERT: G 147 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6850 (mm-30) REVERT: G 162 LYS cc_start: 0.8515 (mttm) cc_final: 0.8177 (mttm) REVERT: G 173 TYR cc_start: 0.8754 (m-80) cc_final: 0.8033 (m-80) REVERT: G 221 MET cc_start: 0.8303 (mmt) cc_final: 0.7918 (mmt) REVERT: G 293 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6849 (mt) REVERT: G 367 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6681 (ttt180) REVERT: G 497 LEU cc_start: 0.8840 (tp) cc_final: 0.8506 (tp) REVERT: G 537 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7780 (t0) REVERT: G 589 LEU cc_start: 0.7874 (tp) cc_final: 0.7427 (mm) REVERT: G 590 VAL cc_start: 0.8091 (m) cc_final: 0.7859 (m) REVERT: G 653 HIS cc_start: 0.6869 (t-90) cc_final: 0.6643 (t-170) REVERT: G 671 HIS cc_start: 0.6627 (m170) cc_final: 0.6190 (t-90) REVERT: G 738 MET cc_start: 0.6422 (ptt) cc_final: 0.6200 (ptt) REVERT: G 760 ASN cc_start: 0.8080 (m-40) cc_final: 0.7833 (m-40) REVERT: G 784 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7707 (mtp-110) REVERT: G 804 GLN cc_start: 0.7541 (tp40) cc_final: 0.7336 (tp-100) REVERT: I 106 GLU cc_start: 0.7610 (tt0) cc_final: 0.7294 (tt0) REVERT: I 124 GLU cc_start: 0.7342 (tp30) cc_final: 0.6487 (tp30) REVERT: K 31 MET cc_start: 0.6155 (mpp) cc_final: 0.5649 (mpp) REVERT: J 1 MET cc_start: 0.3000 (tpt) cc_final: 0.2550 (tmm) REVERT: J 112 LEU cc_start: 0.6351 (pp) cc_final: 0.6004 (mt) REVERT: A 78 PHE cc_start: 0.8375 (m-80) cc_final: 0.8012 (m-80) REVERT: A 107 ILE cc_start: 0.8106 (pt) cc_final: 0.7844 (pt) REVERT: H 88 MET cc_start: 0.5580 (mpp) cc_final: 0.3975 (mmt) REVERT: H 311 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5109 (mp) REVERT: M 67 PHE cc_start: 0.2011 (t80) cc_final: 0.1578 (t80) REVERT: M 75 PHE cc_start: 0.6211 (m-80) cc_final: 0.5931 (m-80) REVERT: M 156 LEU cc_start: 0.6617 (tp) cc_final: 0.6361 (tp) REVERT: M 336 LEU cc_start: 0.7655 (tp) cc_final: 0.5781 (tp) REVERT: M 356 PHE cc_start: 0.4641 (m-10) cc_final: 0.4336 (m-10) REVERT: L 137 LEU cc_start: 0.0717 (OUTLIER) cc_final: 0.0421 (mp) REVERT: L 158 TYR cc_start: 0.4746 (p90) cc_final: 0.4458 (p90) REVERT: L 191 GLU cc_start: 0.6278 (tp30) cc_final: 0.5762 (tp30) REVERT: L 195 LEU cc_start: 0.1390 (OUTLIER) cc_final: -0.0873 (mt) REVERT: L 200 MET cc_start: 0.6842 (tpp) cc_final: 0.6538 (tpt) REVERT: L 214 MET cc_start: 0.3684 (tmm) cc_final: 0.3437 (tmm) REVERT: L 296 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6411 (p90) REVERT: L 319 MET cc_start: 0.4983 (mmm) cc_final: 0.4691 (mmm) REVERT: L 592 ARG cc_start: 0.4965 (mtt90) cc_final: 0.3581 (ttp-110) REVERT: L 594 TYR cc_start: 0.5431 (m-10) cc_final: 0.4713 (m-10) REVERT: N 62 ASP cc_start: 0.2596 (m-30) cc_final: 0.2025 (m-30) REVERT: N 74 MET cc_start: 0.5403 (mtp) cc_final: 0.4953 (ptt) REVERT: N 286 LEU cc_start: 0.8088 (mp) cc_final: 0.7818 (mp) REVERT: N 314 ILE cc_start: 0.4171 (tp) cc_final: 0.3950 (tp) REVERT: N 379 MET cc_start: 0.6158 (mmt) cc_final: 0.5292 (mmt) REVERT: N 427 ARG cc_start: 0.6988 (mtm180) cc_final: 0.6377 (mmm160) outliers start: 137 outliers final: 83 residues processed: 1174 average time/residue: 0.5046 time to fit residues: 945.4003 Evaluate side-chains 1125 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1032 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 472 VAL Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 344 optimal weight: 40.0000 chunk 281 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 414 optimal weight: 8.9990 chunk 448 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 411 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 332 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 213 ASN D 74 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN G 865 ASN G 899 HIS I 128 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS L 270 HIS L 570 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 36088 Z= 0.345 Angle : 0.724 12.669 49115 Z= 0.369 Chirality : 0.048 0.338 5554 Planarity : 0.006 0.074 6255 Dihedral : 5.882 167.923 4997 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 5.13 % Allowed : 17.63 % Favored : 77.24 % 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: -0.49 (0.12), residues: 4573 helix: 0.36 (0.10), residues: 2457 sheet: -0.37 (0.30), residues: 307 loop : -1.18 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 260 HIS 0.017 0.002 HIS L 270 PHE 0.049 0.002 PHE H 278 TYR 0.046 0.002 TYR L 189 ARG 0.008 0.001 ARG G 242 *********************** 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 1255 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1074 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7648 (t60) cc_final: 0.7283 (t60) REVERT: B 57 TYR cc_start: 0.7268 (t80) cc_final: 0.6913 (t80) REVERT: B 103 PHE cc_start: 0.5963 (m-80) cc_final: 0.5649 (m-80) REVERT: B 204 LYS cc_start: 0.7498 (ptpp) cc_final: 0.7127 (ptpp) REVERT: D 48 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (pt) REVERT: D 51 GLU cc_start: 0.7785 (pm20) cc_final: 0.6614 (pm20) REVERT: D 60 LEU cc_start: 0.8491 (mp) cc_final: 0.8280 (mp) REVERT: D 153 ARG cc_start: 0.4949 (mtp85) cc_final: 0.4453 (mtp85) REVERT: D 447 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6190 (p0) REVERT: D 524 MET cc_start: 0.8201 (mmm) cc_final: 0.7942 (mmm) REVERT: D 553 TYR cc_start: 0.8220 (t80) cc_final: 0.7535 (t80) REVERT: E 18 GLU cc_start: 0.7579 (mp0) cc_final: 0.7067 (pm20) REVERT: E 45 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8022 (tptp) REVERT: E 90 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7202 (mtm-85) REVERT: E 134 LEU cc_start: 0.8792 (mt) cc_final: 0.8550 (mt) REVERT: F 252 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: G 78 SER cc_start: 0.9133 (t) cc_final: 0.8568 (p) REVERT: G 83 GLU cc_start: 0.7874 (tp30) cc_final: 0.7435 (tp30) REVERT: G 162 LYS cc_start: 0.8623 (mttm) cc_final: 0.8151 (mttm) REVERT: G 221 MET cc_start: 0.8472 (mmt) cc_final: 0.8230 (mmt) REVERT: G 293 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7412 (mt) REVERT: G 311 LYS cc_start: 0.7529 (tttt) cc_final: 0.6874 (tttm) REVERT: G 537 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7902 (t0) REVERT: G 572 HIS cc_start: 0.7599 (m-70) cc_final: 0.7085 (m170) REVERT: G 621 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7762 (mt) REVERT: G 671 HIS cc_start: 0.6944 (m170) cc_final: 0.6452 (t-90) REVERT: G 683 LEU cc_start: 0.9285 (mt) cc_final: 0.8968 (mt) REVERT: G 726 GLN cc_start: 0.7065 (mt0) cc_final: 0.6600 (mt0) REVERT: G 743 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: G 784 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7835 (mtp85) REVERT: G 804 GLN cc_start: 0.7569 (tp40) cc_final: 0.7268 (tm-30) REVERT: G 832 GLN cc_start: 0.6530 (mm-40) cc_final: 0.6158 (mm-40) REVERT: I 124 GLU cc_start: 0.7451 (tp30) cc_final: 0.6646 (tp30) REVERT: K 36 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6174 (mm-30) REVERT: K 53 TRP cc_start: 0.6673 (m100) cc_final: 0.6402 (m100) REVERT: K 57 ASP cc_start: 0.7654 (t70) cc_final: 0.7176 (t70) REVERT: J 112 LEU cc_start: 0.6388 (pp) cc_final: 0.6155 (tp) REVERT: J 134 PHE cc_start: 0.6885 (t80) cc_final: 0.6572 (t80) REVERT: H 88 MET cc_start: 0.6097 (mpp) cc_final: 0.4734 (mmt) REVERT: H 311 ILE cc_start: 0.5440 (OUTLIER) cc_final: 0.5003 (mp) REVERT: M 75 PHE cc_start: 0.6417 (m-80) cc_final: 0.6210 (m-80) REVERT: M 103 LEU cc_start: 0.8398 (tp) cc_final: 0.8170 (tp) REVERT: M 215 MET cc_start: 0.4656 (mmm) cc_final: 0.4369 (mpp) REVERT: M 315 ILE cc_start: 0.1442 (mt) cc_final: 0.1206 (mt) REVERT: M 356 PHE cc_start: 0.4998 (m-10) cc_final: 0.4723 (m-10) REVERT: M 463 ARG cc_start: 0.5916 (ppt170) cc_final: 0.5351 (tmm160) REVERT: L 22 ARG cc_start: 0.5710 (mmm160) cc_final: 0.5368 (mmm160) REVERT: L 191 GLU cc_start: 0.6398 (tp30) cc_final: 0.5960 (tp30) REVERT: L 195 LEU cc_start: -0.0554 (OUTLIER) cc_final: -0.2768 (mt) REVERT: L 214 MET cc_start: 0.4104 (tmm) cc_final: 0.3638 (tmm) REVERT: L 275 MET cc_start: 0.0868 (mmt) cc_final: -0.0338 (mmt) REVERT: L 296 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.6033 (p90) REVERT: L 306 ARG cc_start: 0.7885 (ptt90) cc_final: 0.7628 (ppt170) REVERT: L 590 TYR cc_start: 0.3890 (m-80) cc_final: 0.3237 (m-80) REVERT: L 592 ARG cc_start: 0.4948 (mtt90) cc_final: 0.3628 (ttp80) REVERT: L 594 TYR cc_start: 0.5495 (m-10) cc_final: 0.4676 (m-10) REVERT: N 74 MET cc_start: 0.5686 (mtp) cc_final: 0.5427 (mtm) REVERT: N 140 PHE cc_start: 0.4879 (m-80) cc_final: 0.4327 (m-80) REVERT: N 286 LEU cc_start: 0.8181 (mp) cc_final: 0.7879 (mp) REVERT: N 314 ILE cc_start: 0.4038 (tp) cc_final: 0.3835 (tp) REVERT: N 379 MET cc_start: 0.6311 (mmt) cc_final: 0.5280 (mmt) REVERT: N 427 ARG cc_start: 0.7256 (mtm180) cc_final: 0.6740 (mmm160) outliers start: 181 outliers final: 120 residues processed: 1147 average time/residue: 0.4567 time to fit residues: 836.1755 Evaluate side-chains 1147 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1017 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 621 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 743 GLN Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 785 LEU Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 840 ILE Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain L residue 65 TRP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 475 ILE Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 416 optimal weight: 9.9990 chunk 440 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 394 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN B 196 ASN ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 150 ASN D 259 GLN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 HIS ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS L 254 HIS L 270 HIS ** L 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS N 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 36088 Z= 0.452 Angle : 0.797 13.510 49115 Z= 0.409 Chirality : 0.052 0.406 5554 Planarity : 0.006 0.099 6255 Dihedral : 6.188 168.474 4993 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.04 % Allowed : 20.32 % Favored : 73.64 % 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: -0.80 (0.12), residues: 4573 helix: 0.19 (0.10), residues: 2476 sheet: -0.89 (0.30), residues: 298 loop : -1.39 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 262 HIS 0.032 0.002 HIS D 74 PHE 0.045 0.003 PHE H 278 TYR 0.026 0.003 TYR M 435 ARG 0.011 0.001 ARG F 39 *********************** 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 1259 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1046 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.7655 (t60) cc_final: 0.7118 (t60) REVERT: B 170 MET cc_start: 0.8528 (ttp) cc_final: 0.8229 (ttp) REVERT: D 48 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7302 (pt) REVERT: D 60 LEU cc_start: 0.8626 (mp) cc_final: 0.8386 (mp) REVERT: D 110 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7966 (mtpp) REVERT: D 305 MET cc_start: 0.8267 (ttp) cc_final: 0.7975 (ttp) REVERT: D 340 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6614 (tm130) REVERT: D 353 ARG cc_start: 0.6669 (mtp85) cc_final: 0.6368 (ptp-170) REVERT: D 447 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6507 (p0) REVERT: D 484 MET cc_start: 0.7580 (tpp) cc_final: 0.7019 (ttm) REVERT: D 497 THR cc_start: 0.9621 (m) cc_final: 0.9001 (p) REVERT: D 524 MET cc_start: 0.8130 (mmm) cc_final: 0.7733 (mmm) REVERT: D 553 TYR cc_start: 0.8315 (t80) cc_final: 0.7514 (t80) REVERT: E 13 GLU cc_start: 0.6208 (tp30) cc_final: 0.5974 (tp30) REVERT: E 18 GLU cc_start: 0.8302 (mp0) cc_final: 0.7552 (pm20) REVERT: E 45 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8087 (tptp) REVERT: E 100 ASN cc_start: 0.6542 (OUTLIER) cc_final: 0.6324 (t0) REVERT: F 1 MET cc_start: 0.6672 (ppp) cc_final: 0.6116 (ppp) REVERT: F 98 THR cc_start: 0.8489 (m) cc_final: 0.8268 (p) REVERT: F 161 MET cc_start: 0.7894 (mmm) cc_final: 0.7590 (ptp) REVERT: F 288 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6659 (mtmm) REVERT: F 358 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7729 (ttp80) REVERT: G 78 SER cc_start: 0.9134 (t) cc_final: 0.8544 (p) REVERT: G 293 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7736 (mt) REVERT: G 367 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6843 (ttt180) REVERT: G 537 ASN cc_start: 0.8395 (t0) cc_final: 0.8126 (t0) REVERT: G 539 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.5923 (mmm) REVERT: G 551 GLU cc_start: 0.6735 (mp0) cc_final: 0.6311 (mp0) REVERT: G 572 HIS cc_start: 0.7998 (m-70) cc_final: 0.7455 (m170) REVERT: G 621 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8666 (mt) REVERT: G 683 LEU cc_start: 0.9246 (mt) cc_final: 0.8942 (mt) REVERT: G 784 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7800 (mtp85) REVERT: G 832 GLN cc_start: 0.6552 (mm-40) cc_final: 0.5871 (mm-40) REVERT: I 47 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6690 (ttm110) REVERT: I 81 GLU cc_start: 0.8539 (tt0) cc_final: 0.8284 (tt0) REVERT: I 124 GLU cc_start: 0.7590 (tp30) cc_final: 0.6626 (tp30) REVERT: J 103 MET cc_start: 0.3592 (OUTLIER) cc_final: 0.3380 (mmm) REVERT: J 134 PHE cc_start: 0.6869 (t80) cc_final: 0.6653 (t80) REVERT: H 88 MET cc_start: 0.5832 (mpp) cc_final: 0.4946 (mmt) REVERT: H 120 LEU cc_start: 0.5388 (mm) cc_final: 0.5117 (tp) REVERT: H 279 MET cc_start: 0.6580 (mpp) cc_final: 0.6028 (mmt) REVERT: H 310 LEU cc_start: 0.6175 (mt) cc_final: 0.5920 (mt) REVERT: H 311 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5499 (mp) REVERT: M 75 PHE cc_start: 0.6997 (m-80) cc_final: 0.6748 (m-80) REVERT: M 118 LEU cc_start: 0.2925 (OUTLIER) cc_final: 0.2612 (tt) REVERT: M 146 MET cc_start: 0.5295 (ppp) cc_final: 0.5057 (ppp) REVERT: M 152 PHE cc_start: 0.5914 (t80) cc_final: 0.5597 (t80) REVERT: M 315 ILE cc_start: 0.1646 (mt) cc_final: 0.1410 (mt) REVERT: M 356 PHE cc_start: 0.5001 (m-10) cc_final: 0.4740 (m-10) REVERT: M 475 LEU cc_start: 0.7629 (pp) cc_final: 0.6037 (tp) REVERT: M 495 ASN cc_start: 0.1618 (OUTLIER) cc_final: 0.1339 (t0) REVERT: L 22 ARG cc_start: 0.5585 (mmm160) cc_final: 0.5291 (mmm160) REVERT: L 156 PHE cc_start: 0.3326 (OUTLIER) cc_final: 0.3122 (m-80) REVERT: L 191 GLU cc_start: 0.6373 (tp30) cc_final: 0.5814 (tp30) REVERT: L 195 LEU cc_start: -0.1626 (OUTLIER) cc_final: -0.3204 (mt) REVERT: L 214 MET cc_start: 0.3638 (tmm) cc_final: 0.3185 (tmm) REVERT: L 215 LEU cc_start: 0.7480 (tp) cc_final: 0.7159 (mt) REVERT: L 239 LEU cc_start: 0.6216 (mp) cc_final: 0.5935 (mm) REVERT: L 258 MET cc_start: -0.4444 (tpt) cc_final: -0.5154 (tpt) REVERT: L 275 MET cc_start: 0.2370 (mmt) cc_final: 0.1305 (mmt) REVERT: L 296 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6077 (p90) REVERT: L 305 LYS cc_start: 0.5494 (mmtt) cc_final: 0.5291 (mmtt) REVERT: L 306 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7452 (ppt170) REVERT: L 319 MET cc_start: 0.5276 (mmm) cc_final: 0.4922 (mmm) REVERT: L 568 MET cc_start: 0.4719 (ptt) cc_final: 0.4083 (ptt) REVERT: L 592 ARG cc_start: 0.4781 (mtt90) cc_final: 0.3657 (ttp80) REVERT: N 42 VAL cc_start: 0.6854 (p) cc_final: 0.6412 (m) REVERT: N 68 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.5941 (tpt-90) REVERT: N 74 MET cc_start: 0.5659 (mtp) cc_final: 0.5397 (mtm) REVERT: N 140 PHE cc_start: 0.5989 (m-80) cc_final: 0.5239 (m-80) REVERT: N 151 ARG cc_start: 0.5714 (ptp-170) cc_final: 0.4922 (ttp-110) REVERT: N 227 THR cc_start: 0.6858 (m) cc_final: 0.6336 (p) REVERT: N 286 LEU cc_start: 0.8034 (mp) cc_final: 0.7694 (mp) REVERT: N 379 MET cc_start: 0.6332 (mmt) cc_final: 0.5193 (mmt) REVERT: N 427 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6663 (mmm160) outliers start: 213 outliers final: 145 residues processed: 1139 average time/residue: 0.5098 time to fit residues: 935.5785 Evaluate side-chains 1175 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1012 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 339 THR Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 593 VAL Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 621 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 791 ASN Chi-restraints excluded: chain G residue 856 THR Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain G residue 903 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 221 TYR Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 156 PHE Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 328 optimal weight: 8.9990 chunk 181 optimal weight: 0.3980 chunk 376 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 395 optimal weight: 50.0000 chunk 111 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN D 259 GLN D 482 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 216 ASN G 766 ASN K 84 HIS ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 270 HIS L 338 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 36088 Z= 0.232 Angle : 0.670 12.922 49115 Z= 0.336 Chirality : 0.044 0.319 5554 Planarity : 0.005 0.071 6255 Dihedral : 5.718 166.532 4986 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.79 % Allowed : 22.96 % Favored : 72.25 % 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: 0.46 (0.10), residues: 2480 sheet: -0.74 (0.30), residues: 300 loop : -1.27 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 106 HIS 0.017 0.002 HIS L 338 PHE 0.048 0.002 PHE H 282 TYR 0.026 0.002 TYR M 435 ARG 0.007 0.001 ARG F 39 *********************** 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 1219 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1050 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8345 (ttp) cc_final: 0.8134 (ttp) REVERT: D 60 LEU cc_start: 0.8519 (mp) cc_final: 0.8300 (mp) REVERT: D 353 ARG cc_start: 0.6544 (mtp85) cc_final: 0.6325 (ptp-170) REVERT: D 392 LYS cc_start: 0.7765 (pttm) cc_final: 0.7266 (mmtm) REVERT: D 524 MET cc_start: 0.8090 (mmm) cc_final: 0.7747 (mmm) REVERT: D 553 TYR cc_start: 0.8252 (t80) cc_final: 0.7411 (t80) REVERT: E 13 GLU cc_start: 0.6135 (tp30) cc_final: 0.5907 (tp30) REVERT: E 18 GLU cc_start: 0.8136 (mp0) cc_final: 0.7504 (pm20) REVERT: E 45 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7969 (tptp) REVERT: E 162 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7457 (mt) REVERT: F 1 MET cc_start: 0.6526 (ppp) cc_final: 0.2329 (tpp) REVERT: F 98 THR cc_start: 0.8473 (m) cc_final: 0.8241 (p) REVERT: F 158 LYS cc_start: 0.7701 (tptt) cc_final: 0.7373 (tppt) REVERT: F 161 MET cc_start: 0.7743 (mmm) cc_final: 0.7367 (ptp) REVERT: F 165 PHE cc_start: 0.7209 (t80) cc_final: 0.6834 (t80) REVERT: F 252 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: F 288 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6778 (mtmm) REVERT: F 332 GLU cc_start: 0.6735 (pt0) cc_final: 0.6493 (pm20) REVERT: G 78 SER cc_start: 0.8965 (t) cc_final: 0.8332 (p) REVERT: G 293 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7650 (mt) REVERT: G 367 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7114 (ttt180) REVERT: G 537 ASN cc_start: 0.8336 (t0) cc_final: 0.7963 (t0) REVERT: G 551 GLU cc_start: 0.6655 (mp0) cc_final: 0.6121 (mp0) REVERT: G 572 HIS cc_start: 0.7901 (m-70) cc_final: 0.7241 (m170) REVERT: G 651 TRP cc_start: 0.7336 (m100) cc_final: 0.6812 (m100) REVERT: G 743 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: G 784 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7782 (mtp85) REVERT: I 47 ARG cc_start: 0.6959 (ttm110) cc_final: 0.6748 (ttm110) REVERT: I 53 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: I 106 GLU cc_start: 0.7716 (tt0) cc_final: 0.7485 (tt0) REVERT: I 124 GLU cc_start: 0.7431 (tp30) cc_final: 0.6494 (tp30) REVERT: J 112 LEU cc_start: 0.6626 (tp) cc_final: 0.6072 (mt) REVERT: J 134 PHE cc_start: 0.6876 (t80) cc_final: 0.6666 (t80) REVERT: A 78 PHE cc_start: 0.8250 (m-80) cc_final: 0.8007 (m-80) REVERT: H 311 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5686 (mp) REVERT: M 118 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.2522 (tt) REVERT: M 356 PHE cc_start: 0.4954 (m-10) cc_final: 0.4634 (m-10) REVERT: M 463 ARG cc_start: 0.7297 (tmm160) cc_final: 0.6922 (ppt170) REVERT: M 475 LEU cc_start: 0.7611 (pp) cc_final: 0.6006 (tp) REVERT: L 22 ARG cc_start: 0.5471 (mmm160) cc_final: 0.5121 (mmm160) REVERT: L 108 ARG cc_start: 0.6286 (mmm160) cc_final: 0.6011 (mmt180) REVERT: L 191 GLU cc_start: 0.6270 (tp30) cc_final: 0.5805 (tp30) REVERT: L 215 LEU cc_start: 0.7565 (tp) cc_final: 0.7237 (mt) REVERT: L 258 MET cc_start: -0.4359 (tpt) cc_final: -0.4846 (tpt) REVERT: L 275 MET cc_start: 0.2442 (mmt) cc_final: 0.1549 (mmt) REVERT: L 296 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6297 (p90) REVERT: L 306 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7384 (ppt170) REVERT: L 592 ARG cc_start: 0.4810 (mtt90) cc_final: 0.3678 (ttp80) REVERT: L 598 MET cc_start: 0.6941 (mmp) cc_final: 0.5095 (mmp) REVERT: L 605 VAL cc_start: 0.3726 (m) cc_final: 0.3210 (t) REVERT: N 68 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.5505 (tpt-90) REVERT: N 140 PHE cc_start: 0.5584 (m-80) cc_final: 0.4933 (m-80) REVERT: N 151 ARG cc_start: 0.5479 (ptp-170) cc_final: 0.4732 (ttp-110) REVERT: N 286 LEU cc_start: 0.7825 (mp) cc_final: 0.7482 (mp) REVERT: N 309 LEU cc_start: 0.7405 (mt) cc_final: 0.6772 (mt) REVERT: N 379 MET cc_start: 0.6377 (mmt) cc_final: 0.5306 (mmt) outliers start: 169 outliers final: 114 residues processed: 1115 average time/residue: 0.4932 time to fit residues: 884.2294 Evaluate side-chains 1141 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1015 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 404 MET Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 702 LEU Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 743 GLN Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain G residue 903 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain M residue 486 LEU Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 475 ILE Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 0.5980 chunk 396 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 258 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 441 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 204 optimal weight: 0.1980 chunk 36 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 107 GLN F 217 ASN G 5 HIS ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 270 HIS L 570 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36088 Z= 0.202 Angle : 0.653 11.976 49115 Z= 0.326 Chirality : 0.043 0.342 5554 Planarity : 0.005 0.077 6255 Dihedral : 5.522 166.467 4986 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.76 % Allowed : 23.95 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.31 (0.12), residues: 4573 helix: 0.60 (0.10), residues: 2480 sheet: -0.79 (0.29), residues: 308 loop : -1.16 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 94 HIS 0.016 0.001 HIS L 270 PHE 0.046 0.002 PHE H 282 TYR 0.025 0.002 TYR M 435 ARG 0.008 0.001 ARG F 39 *********************** 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 1211 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1043 time to evaluate : 3.905 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: D 80 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7675 (mt) REVERT: D 392 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7269 (mmtm) REVERT: D 464 MET cc_start: 0.7001 (tpt) cc_final: 0.6693 (tpt) REVERT: D 497 THR cc_start: 0.9594 (m) cc_final: 0.9323 (p) REVERT: D 524 MET cc_start: 0.8075 (mmm) cc_final: 0.7524 (mmm) REVERT: D 553 TYR cc_start: 0.8237 (t80) cc_final: 0.7402 (t80) REVERT: E 13 GLU cc_start: 0.6133 (tp30) cc_final: 0.5925 (tp30) REVERT: E 18 GLU cc_start: 0.7905 (mp0) cc_final: 0.7290 (pm20) REVERT: E 45 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7924 (tptp) REVERT: E 144 MET cc_start: 0.8045 (ptm) cc_final: 0.7829 (ptm) REVERT: E 162 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7426 (mt) REVERT: F 1 MET cc_start: 0.6405 (ppp) cc_final: 0.2085 (tpp) REVERT: F 98 THR cc_start: 0.8431 (m) cc_final: 0.8209 (p) REVERT: F 158 LYS cc_start: 0.7572 (tptt) cc_final: 0.7286 (tppt) REVERT: F 161 MET cc_start: 0.7645 (mmm) cc_final: 0.7048 (ptp) REVERT: F 165 PHE cc_start: 0.7140 (t80) cc_final: 0.6860 (t80) REVERT: F 252 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: F 262 TRP cc_start: 0.7862 (m-90) cc_final: 0.7281 (m-10) REVERT: F 332 GLU cc_start: 0.6589 (pt0) cc_final: 0.6378 (pm20) REVERT: F 415 PHE cc_start: 0.6454 (m-10) cc_final: 0.6011 (m-10) REVERT: G 94 TRP cc_start: 0.8717 (m-10) cc_final: 0.8459 (m-90) REVERT: G 361 ILE cc_start: 0.7536 (mm) cc_final: 0.7299 (mt) REVERT: G 427 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (m-70) REVERT: G 537 ASN cc_start: 0.8329 (t0) cc_final: 0.8001 (t0) REVERT: G 551 GLU cc_start: 0.6623 (mp0) cc_final: 0.5941 (mp0) REVERT: G 572 HIS cc_start: 0.7929 (m-70) cc_final: 0.7297 (m170) REVERT: G 743 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: I 53 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: I 124 GLU cc_start: 0.7418 (tp30) cc_final: 0.6465 (tp30) REVERT: I 133 GLU cc_start: 0.7305 (mp0) cc_final: 0.6890 (mp0) REVERT: K 31 MET cc_start: 0.5803 (mpp) cc_final: 0.5359 (mpp) REVERT: J 72 MET cc_start: 0.6126 (tpt) cc_final: 0.3756 (ttm) REVERT: J 112 LEU cc_start: 0.6330 (tp) cc_final: 0.5932 (mt) REVERT: J 134 PHE cc_start: 0.6858 (t80) cc_final: 0.6627 (t80) REVERT: H 237 PHE cc_start: 0.6059 (m-80) cc_final: 0.5633 (m-80) REVERT: H 279 MET cc_start: 0.6521 (mpp) cc_final: 0.5949 (mmt) REVERT: H 311 ILE cc_start: 0.6111 (OUTLIER) cc_final: 0.5667 (mp) REVERT: M 75 PHE cc_start: 0.6827 (m-80) cc_final: 0.6524 (m-80) REVERT: M 118 LEU cc_start: 0.2838 (pp) cc_final: 0.2527 (tt) REVERT: M 276 LEU cc_start: 0.6734 (mm) cc_final: 0.6529 (mp) REVERT: M 463 ARG cc_start: 0.7395 (tmm160) cc_final: 0.6696 (ppt170) REVERT: M 475 LEU cc_start: 0.7557 (pp) cc_final: 0.6042 (tp) REVERT: M 501 VAL cc_start: 0.4085 (t) cc_final: 0.3793 (p) REVERT: L 22 ARG cc_start: 0.5034 (mmm160) cc_final: 0.4774 (mmm160) REVERT: L 191 GLU cc_start: 0.6467 (tp30) cc_final: 0.6025 (tp30) REVERT: L 214 MET cc_start: 0.3735 (tmm) cc_final: 0.3476 (tmm) REVERT: L 215 LEU cc_start: 0.7553 (tp) cc_final: 0.7160 (mt) REVERT: L 275 MET cc_start: 0.2835 (mmt) cc_final: 0.2029 (mmt) REVERT: L 296 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6233 (p90) REVERT: L 306 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7333 (ppt170) REVERT: L 313 MET cc_start: 0.5032 (mtp) cc_final: 0.4733 (mtp) REVERT: L 592 ARG cc_start: 0.4877 (mtt90) cc_final: 0.3683 (ttp80) REVERT: L 598 MET cc_start: 0.6826 (mmp) cc_final: 0.5226 (mmp) REVERT: L 605 VAL cc_start: 0.3242 (m) cc_final: 0.2576 (t) REVERT: N 68 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5795 (tpt-90) REVERT: N 140 PHE cc_start: 0.4677 (m-80) cc_final: 0.4180 (m-80) REVERT: N 151 ARG cc_start: 0.5479 (ptp-170) cc_final: 0.4752 (ttp-110) REVERT: N 286 LEU cc_start: 0.7786 (mp) cc_final: 0.7437 (mp) REVERT: N 321 MET cc_start: 0.3979 (pmm) cc_final: 0.2981 (pmm) REVERT: N 379 MET cc_start: 0.6345 (mmt) cc_final: 0.5290 (mmt) outliers start: 168 outliers final: 128 residues processed: 1107 average time/residue: 0.4903 time to fit residues: 874.2952 Evaluate side-chains 1162 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1023 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 702 LEU Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 743 GLN Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 899 HIS Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain G residue 903 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Chi-restraints excluded: chain N residue 480 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 251 optimal weight: 9.9990 chunk 322 optimal weight: 0.0050 chunk 249 optimal weight: 0.9980 chunk 371 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 439 optimal weight: 8.9990 chunk 275 optimal weight: 0.2980 chunk 267 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS E 100 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36088 Z= 0.187 Angle : 0.663 13.733 49115 Z= 0.329 Chirality : 0.043 0.337 5554 Planarity : 0.005 0.077 6255 Dihedral : 5.390 166.171 4986 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.20 % Allowed : 25.51 % Favored : 70.29 % 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: -0.17 (0.12), residues: 4573 helix: 0.68 (0.10), residues: 2482 sheet: -0.66 (0.29), residues: 302 loop : -1.07 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 106 HIS 0.017 0.001 HIS G 653 PHE 0.051 0.002 PHE H 282 TYR 0.026 0.002 TYR M 435 ARG 0.015 0.001 ARG G 802 *********************** 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 1184 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1036 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 LYS cc_start: 0.7656 (ptpp) cc_final: 0.7387 (ptpp) REVERT: D 80 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (mm) REVERT: D 392 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7114 (mmmt) REVERT: D 524 MET cc_start: 0.8230 (mmm) cc_final: 0.7877 (mmm) REVERT: D 553 TYR cc_start: 0.8216 (t80) cc_final: 0.7423 (t80) REVERT: E 18 GLU cc_start: 0.7867 (mp0) cc_final: 0.7458 (mp0) REVERT: E 45 LYS cc_start: 0.8256 (tmmt) cc_final: 0.7963 (tptp) REVERT: E 60 ASP cc_start: 0.7584 (t0) cc_final: 0.7044 (p0) REVERT: E 82 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: E 162 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7406 (mt) REVERT: F 1 MET cc_start: 0.6521 (ppp) cc_final: 0.2176 (tpp) REVERT: F 98 THR cc_start: 0.8411 (m) cc_final: 0.8151 (p) REVERT: F 161 MET cc_start: 0.7587 (mmm) cc_final: 0.7055 (ptp) REVERT: F 235 TRP cc_start: 0.4596 (t60) cc_final: 0.4367 (t60) REVERT: F 252 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: F 262 TRP cc_start: 0.8045 (m-90) cc_final: 0.7510 (m-90) REVERT: G 94 TRP cc_start: 0.8685 (m-10) cc_final: 0.8428 (m-90) REVERT: G 361 ILE cc_start: 0.7492 (mm) cc_final: 0.7268 (mt) REVERT: G 537 ASN cc_start: 0.8274 (t0) cc_final: 0.7943 (t0) REVERT: G 572 HIS cc_start: 0.8002 (m-70) cc_final: 0.7379 (m-70) REVERT: G 743 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: G 886 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6856 (mmm) REVERT: I 79 LYS cc_start: 0.8684 (tmmt) cc_final: 0.8409 (ttpt) REVERT: I 124 GLU cc_start: 0.7320 (tp30) cc_final: 0.6392 (tp30) REVERT: K 98 MET cc_start: 0.3634 (OUTLIER) cc_final: 0.3354 (ppp) REVERT: J 72 MET cc_start: 0.6237 (tpt) cc_final: 0.4028 (ttm) REVERT: J 112 LEU cc_start: 0.6328 (tp) cc_final: 0.5936 (mt) REVERT: J 134 PHE cc_start: 0.6842 (t80) cc_final: 0.6622 (t80) REVERT: H 88 MET cc_start: 0.4872 (mtp) cc_final: 0.4377 (mmt) REVERT: H 237 PHE cc_start: 0.5992 (m-80) cc_final: 0.5579 (m-80) REVERT: H 311 ILE cc_start: 0.6325 (OUTLIER) cc_final: 0.5785 (mp) REVERT: M 63 TRP cc_start: 0.4808 (m-90) cc_final: 0.3160 (m-90) REVERT: M 118 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.2122 (tt) REVERT: M 291 MET cc_start: 0.7762 (mmp) cc_final: 0.7207 (mmp) REVERT: M 374 MET cc_start: 0.5326 (pmm) cc_final: 0.4763 (pmm) REVERT: M 415 PHE cc_start: 0.5695 (t80) cc_final: 0.4846 (t80) REVERT: M 463 ARG cc_start: 0.6844 (tmm160) cc_final: 0.6285 (tmm160) REVERT: M 466 PHE cc_start: 0.6770 (t80) cc_final: 0.6529 (t80) REVERT: M 475 LEU cc_start: 0.7450 (pp) cc_final: 0.6111 (tp) REVERT: M 501 VAL cc_start: 0.4018 (t) cc_final: 0.3767 (p) REVERT: L 22 ARG cc_start: 0.4936 (mmm160) cc_final: 0.4671 (mmm160) REVERT: L 73 PHE cc_start: 0.5503 (OUTLIER) cc_final: 0.4943 (m-10) REVERT: L 191 GLU cc_start: 0.6236 (tp30) cc_final: 0.5885 (tp30) REVERT: L 214 MET cc_start: 0.3286 (tmm) cc_final: 0.2604 (tmm) REVERT: L 215 LEU cc_start: 0.7543 (tp) cc_final: 0.7111 (mt) REVERT: L 275 MET cc_start: 0.2393 (mmt) cc_final: 0.1737 (mmt) REVERT: L 305 LYS cc_start: 0.4867 (mmtt) cc_final: 0.3084 (tmtt) REVERT: L 306 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7319 (ppt170) REVERT: L 587 GLU cc_start: 0.1266 (tt0) cc_final: 0.0895 (tp30) REVERT: L 592 ARG cc_start: 0.4325 (mtt90) cc_final: 0.3169 (ttp80) REVERT: L 605 VAL cc_start: 0.3125 (m) cc_final: 0.2357 (t) REVERT: N 68 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5790 (tpt-90) REVERT: N 140 PHE cc_start: 0.4742 (m-80) cc_final: 0.4194 (m-80) REVERT: N 151 ARG cc_start: 0.5396 (ptp-170) cc_final: 0.4777 (ttp-110) REVERT: N 227 THR cc_start: 0.6268 (m) cc_final: 0.5965 (p) REVERT: N 286 LEU cc_start: 0.7683 (mp) cc_final: 0.7390 (mp) REVERT: N 321 MET cc_start: 0.4429 (pmm) cc_final: 0.3563 (pmm) REVERT: N 379 MET cc_start: 0.6314 (mmt) cc_final: 0.5294 (mmt) REVERT: N 427 ARG cc_start: 0.6586 (mmm160) cc_final: 0.6075 (mmm160) outliers start: 148 outliers final: 114 residues processed: 1098 average time/residue: 0.5004 time to fit residues: 878.8234 Evaluate side-chains 1142 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1015 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 702 LEU Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 743 GLN Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 132 optimal weight: 0.0870 chunk 86 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 217 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 overall best weight: 1.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN G 216 ASN ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS G 766 ASN ** G 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 36088 Z= 0.233 Angle : 0.685 13.508 49115 Z= 0.341 Chirality : 0.045 0.291 5554 Planarity : 0.005 0.076 6255 Dihedral : 5.421 165.946 4984 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.76 % Allowed : 26.08 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.12), residues: 4573 helix: 0.71 (0.10), residues: 2463 sheet: -0.82 (0.29), residues: 311 loop : -1.10 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 106 HIS 0.019 0.001 HIS G 653 PHE 0.068 0.002 PHE L 186 TYR 0.026 0.002 TYR M 435 ARG 0.011 0.001 ARG D 403 *********************** 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 1196 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1028 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.8939 (mp) cc_final: 0.8498 (mt) REVERT: B 179 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.4766 (tp30) REVERT: D 264 TYR cc_start: 0.8535 (t80) cc_final: 0.8310 (t80) REVERT: D 392 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7106 (mmmt) REVERT: D 553 TYR cc_start: 0.8230 (t80) cc_final: 0.7358 (t80) REVERT: E 45 LYS cc_start: 0.8272 (tmmt) cc_final: 0.7977 (tptp) REVERT: E 82 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: E 162 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7481 (mt) REVERT: F 1 MET cc_start: 0.7111 (ppp) cc_final: 0.2666 (tpp) REVERT: F 158 LYS cc_start: 0.7754 (tptt) cc_final: 0.7467 (tppt) REVERT: F 161 MET cc_start: 0.7464 (mmm) cc_final: 0.7067 (ptp) REVERT: F 235 TRP cc_start: 0.4733 (OUTLIER) cc_final: 0.4492 (t60) REVERT: F 252 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: F 262 TRP cc_start: 0.7831 (m-90) cc_final: 0.7420 (m-90) REVERT: G 94 TRP cc_start: 0.8795 (m-10) cc_final: 0.8522 (m-90) REVERT: G 221 MET cc_start: 0.8627 (mmt) cc_final: 0.7741 (mmm) REVERT: G 508 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6937 (mm-30) REVERT: G 537 ASN cc_start: 0.8356 (t0) cc_final: 0.8044 (t0) REVERT: G 651 TRP cc_start: 0.7446 (m100) cc_final: 0.7075 (m100) REVERT: G 886 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: I 79 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8456 (ttpt) REVERT: I 124 GLU cc_start: 0.7375 (tp30) cc_final: 0.6464 (tp30) REVERT: J 5 PHE cc_start: 0.3936 (OUTLIER) cc_final: 0.2187 (m-80) REVERT: J 72 MET cc_start: 0.6450 (tpt) cc_final: 0.4156 (ttm) REVERT: J 112 LEU cc_start: 0.6290 (tp) cc_final: 0.5874 (mt) REVERT: J 134 PHE cc_start: 0.6917 (t80) cc_final: 0.6695 (t80) REVERT: H 83 PHE cc_start: 0.6997 (t80) cc_final: 0.6646 (t80) REVERT: H 88 MET cc_start: 0.4706 (mtp) cc_final: 0.4344 (mmt) REVERT: H 143 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3862 (tp) REVERT: H 237 PHE cc_start: 0.6083 (m-80) cc_final: 0.5647 (m-80) REVERT: H 311 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.5884 (mp) REVERT: M 63 TRP cc_start: 0.4853 (m-90) cc_final: 0.3171 (m-90) REVERT: M 74 ARG cc_start: 0.6489 (mtp-110) cc_final: 0.5675 (ttm-80) REVERT: M 118 LEU cc_start: 0.2836 (OUTLIER) cc_final: 0.2538 (tt) REVERT: M 276 LEU cc_start: 0.6759 (mm) cc_final: 0.6343 (mp) REVERT: M 374 MET cc_start: 0.4790 (pmm) cc_final: 0.4156 (pmm) REVERT: M 460 MET cc_start: -0.0547 (ptt) cc_final: -0.0870 (ptm) REVERT: M 462 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5327 (tp) REVERT: M 463 ARG cc_start: 0.6949 (tmm160) cc_final: 0.6236 (tmm160) REVERT: M 475 LEU cc_start: 0.7201 (pp) cc_final: 0.5977 (tp) REVERT: M 501 VAL cc_start: 0.3528 (t) cc_final: 0.3219 (p) REVERT: L 22 ARG cc_start: 0.5161 (mmm160) cc_final: 0.4838 (mmm160) REVERT: L 73 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5531 (m-10) REVERT: L 82 ASP cc_start: -0.0942 (t70) cc_final: -0.1184 (t0) REVERT: L 191 GLU cc_start: 0.5967 (tp30) cc_final: 0.5470 (tp30) REVERT: L 214 MET cc_start: 0.3020 (tmm) cc_final: 0.2324 (tmm) REVERT: L 215 LEU cc_start: 0.7572 (tp) cc_final: 0.7099 (mt) REVERT: L 275 MET cc_start: 0.1975 (mmt) cc_final: 0.1434 (mmt) REVERT: L 306 ARG cc_start: 0.7660 (ptt90) cc_final: 0.4463 (mpp-170) REVERT: L 587 GLU cc_start: 0.1161 (tt0) cc_final: 0.0837 (tp30) REVERT: L 592 ARG cc_start: 0.4285 (mtt90) cc_final: 0.3032 (ptt90) REVERT: L 598 MET cc_start: 0.6912 (mmp) cc_final: 0.5783 (mmp) REVERT: L 605 VAL cc_start: 0.3555 (m) cc_final: 0.3039 (t) REVERT: N 68 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5517 (tpt-90) REVERT: N 140 PHE cc_start: 0.4542 (m-80) cc_final: 0.4126 (m-80) REVERT: N 151 ARG cc_start: 0.5339 (ptp-170) cc_final: 0.4676 (ttp-110) REVERT: N 227 THR cc_start: 0.6293 (m) cc_final: 0.5921 (p) REVERT: N 286 LEU cc_start: 0.7565 (mp) cc_final: 0.7275 (mp) REVERT: N 300 TYR cc_start: 0.6242 (m-10) cc_final: 0.5942 (m-80) REVERT: N 321 MET cc_start: 0.4310 (pmm) cc_final: 0.3418 (pmm) REVERT: N 379 MET cc_start: 0.6386 (mmt) cc_final: 0.5334 (mmt) outliers start: 168 outliers final: 142 residues processed: 1097 average time/residue: 0.4911 time to fit residues: 866.7795 Evaluate side-chains 1156 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1000 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 702 LEU Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 196 HIS Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 477 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 6.9990 chunk 421 optimal weight: 8.9990 chunk 384 optimal weight: 9.9990 chunk 409 optimal weight: 3.9990 chunk 420 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 178 optimal weight: 0.0970 chunk 321 optimal weight: 20.0000 chunk 125 optimal weight: 0.2980 chunk 370 optimal weight: 10.0000 chunk 387 optimal weight: 50.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 52 ASN B 167 GLN D 397 ASN F 83 ASN G 138 GLN G 325 ASN G 503 ASN ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS L 270 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 36088 Z= 0.448 Angle : 0.840 14.413 49115 Z= 0.429 Chirality : 0.054 0.423 5554 Planarity : 0.006 0.080 6255 Dihedral : 6.085 165.712 4984 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.75 % Allowed : 25.48 % Favored : 68.76 % Cbeta Deviations : 0.02 % 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: -0.74 (0.12), residues: 4573 helix: 0.33 (0.10), residues: 2467 sheet: -1.04 (0.30), residues: 291 loop : -1.48 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 53 HIS 0.017 0.002 HIS G 653 PHE 0.074 0.003 PHE L 320 TYR 0.030 0.003 TYR E 102 ARG 0.012 0.001 ARG D 403 *********************** 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 1226 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1023 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4835 (tp30) REVERT: D 51 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: D 140 LEU cc_start: 0.8158 (mt) cc_final: 0.7888 (mt) REVERT: D 264 TYR cc_start: 0.8759 (t80) cc_final: 0.8449 (t80) REVERT: D 305 MET cc_start: 0.8274 (ttp) cc_final: 0.8019 (ttp) REVERT: D 392 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7414 (mmmt) REVERT: D 460 TYR cc_start: 0.7163 (t80) cc_final: 0.6580 (t80) REVERT: D 553 TYR cc_start: 0.8222 (t80) cc_final: 0.7278 (t80) REVERT: E 45 LYS cc_start: 0.8372 (tmmt) cc_final: 0.8040 (tptp) REVERT: E 52 ASP cc_start: 0.8414 (t0) cc_final: 0.8102 (p0) REVERT: E 82 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: E 90 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6738 (ptt-90) REVERT: F 1 MET cc_start: 0.7240 (ppp) cc_final: 0.2784 (tpp) REVERT: F 158 LYS cc_start: 0.7895 (tptt) cc_final: 0.7661 (tppt) REVERT: F 161 MET cc_start: 0.7216 (mmm) cc_final: 0.6962 (mtp) REVERT: F 252 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: G 21 GLU cc_start: 0.8411 (pt0) cc_final: 0.8209 (pt0) REVERT: G 193 PHE cc_start: 0.8267 (m-80) cc_final: 0.8004 (m-10) REVERT: G 293 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8101 (mt) REVERT: G 508 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7144 (mm-30) REVERT: G 537 ASN cc_start: 0.8536 (t0) cc_final: 0.8246 (t0) REVERT: G 572 HIS cc_start: 0.7995 (m-70) cc_final: 0.7433 (m170) REVERT: G 651 TRP cc_start: 0.7760 (m100) cc_final: 0.7378 (m100) REVERT: G 683 LEU cc_start: 0.9173 (mt) cc_final: 0.8821 (mt) REVERT: G 862 TYR cc_start: 0.5809 (t80) cc_final: 0.5362 (t80) REVERT: K 31 MET cc_start: 0.6164 (mpp) cc_final: 0.5631 (mpp) REVERT: K 57 ASP cc_start: 0.8477 (t0) cc_final: 0.8217 (t0) REVERT: J 5 PHE cc_start: 0.4079 (OUTLIER) cc_final: 0.2440 (m-80) REVERT: J 72 MET cc_start: 0.5960 (tpt) cc_final: 0.3738 (ttm) REVERT: J 134 PHE cc_start: 0.7184 (t80) cc_final: 0.6976 (t80) REVERT: H 83 PHE cc_start: 0.6942 (t80) cc_final: 0.6651 (t80) REVERT: H 310 LEU cc_start: 0.6387 (mt) cc_final: 0.6069 (mt) REVERT: H 311 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5413 (mp) REVERT: M 35 THR cc_start: 0.4829 (t) cc_final: 0.4626 (p) REVERT: M 151 TYR cc_start: 0.2783 (t80) cc_final: 0.1782 (t80) REVERT: M 211 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.3929 (tp) REVERT: M 374 MET cc_start: 0.4816 (pmm) cc_final: 0.4050 (pmm) REVERT: M 460 MET cc_start: -0.0186 (ptt) cc_final: -0.0448 (ttt) REVERT: M 462 LEU cc_start: 0.6946 (tt) cc_final: 0.5921 (tp) REVERT: M 475 LEU cc_start: 0.7028 (pp) cc_final: 0.5896 (tp) REVERT: M 501 VAL cc_start: 0.3997 (t) cc_final: 0.3696 (p) REVERT: L 22 ARG cc_start: 0.4883 (mmm160) cc_final: 0.4512 (mmm160) REVERT: L 73 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: L 82 ASP cc_start: -0.0495 (t70) cc_final: -0.0723 (t0) REVERT: L 191 GLU cc_start: 0.5742 (tp30) cc_final: 0.5224 (tp30) REVERT: L 214 MET cc_start: 0.2644 (tmm) cc_final: 0.2016 (tmm) REVERT: L 215 LEU cc_start: 0.7536 (tp) cc_final: 0.7006 (mt) REVERT: L 275 MET cc_start: 0.2031 (mmt) cc_final: 0.1557 (mmt) REVERT: L 305 LYS cc_start: 0.5217 (tptt) cc_final: 0.4883 (tptt) REVERT: L 313 MET cc_start: 0.4360 (mtp) cc_final: 0.4122 (mtt) REVERT: L 569 MET cc_start: 0.5863 (mmm) cc_final: 0.5647 (mmm) REVERT: L 592 ARG cc_start: 0.4369 (mtt90) cc_final: 0.3075 (ptt90) REVERT: N 42 VAL cc_start: 0.6783 (p) cc_final: 0.6375 (m) REVERT: N 67 MET cc_start: 0.3515 (ptt) cc_final: 0.3066 (ptt) REVERT: N 68 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6112 (tpt-90) REVERT: N 140 PHE cc_start: 0.6103 (m-80) cc_final: 0.5569 (m-80) REVERT: N 151 ARG cc_start: 0.6004 (ptp-170) cc_final: 0.5192 (ttp-110) REVERT: N 227 THR cc_start: 0.6028 (m) cc_final: 0.5664 (p) REVERT: N 286 LEU cc_start: 0.7992 (mp) cc_final: 0.7513 (mp) REVERT: N 289 LEU cc_start: 0.5305 (mp) cc_final: 0.4816 (tt) REVERT: N 321 MET cc_start: 0.4289 (pmm) cc_final: 0.3443 (pmm) REVERT: N 379 MET cc_start: 0.6346 (mmt) cc_final: 0.5247 (mmt) REVERT: N 427 ARG cc_start: 0.6648 (mmm160) cc_final: 0.6278 (mmm160) outliers start: 203 outliers final: 157 residues processed: 1106 average time/residue: 0.5088 time to fit residues: 916.6568 Evaluate side-chains 1177 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1009 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 355 HIS Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain G residue 404 MET Chi-restraints excluded: chain G residue 427 HIS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 804 GLN Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain G residue 903 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 247 LYS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 433 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 454 optimal weight: 0.9980 chunk 418 optimal weight: 0.1980 chunk 361 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 279 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS G 138 GLN G 216 ASN ** G 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 766 ASN ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36088 Z= 0.221 Angle : 0.733 13.294 49115 Z= 0.366 Chirality : 0.046 0.350 5554 Planarity : 0.005 0.159 6255 Dihedral : 5.627 164.843 4984 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.74 % Allowed : 28.15 % Favored : 68.11 % 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: -0.41 (0.12), residues: 4573 helix: 0.56 (0.11), residues: 2452 sheet: -0.87 (0.30), residues: 289 loop : -1.25 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 106 HIS 0.015 0.001 HIS L 270 PHE 0.061 0.002 PHE H 282 TYR 0.027 0.002 TYR M 435 ARG 0.018 0.001 ARG F 144 ********************** 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 1160 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1028 time to evaluate : 3.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ARG cc_start: 0.7743 (mmt180) cc_final: 0.7480 (mmt180) REVERT: D 264 TYR cc_start: 0.8666 (t80) cc_final: 0.8442 (t80) REVERT: D 338 ASP cc_start: 0.6719 (t0) cc_final: 0.6231 (t0) REVERT: D 392 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7234 (mmtm) REVERT: D 524 MET cc_start: 0.8398 (mmm) cc_final: 0.8002 (mmm) REVERT: D 553 TYR cc_start: 0.8295 (t80) cc_final: 0.7186 (t80) REVERT: E 45 LYS cc_start: 0.8273 (tmmt) cc_final: 0.7996 (tptt) REVERT: E 52 ASP cc_start: 0.8254 (t0) cc_final: 0.8042 (p0) REVERT: E 82 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: F 1 MET cc_start: 0.7186 (ppp) cc_final: 0.2776 (tpp) REVERT: F 161 MET cc_start: 0.7153 (mmm) cc_final: 0.6888 (mtp) REVERT: F 178 TYR cc_start: 0.8366 (t80) cc_final: 0.7652 (t80) REVERT: F 252 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: F 262 TRP cc_start: 0.8074 (m-90) cc_final: 0.7433 (m-10) REVERT: G 293 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7867 (mt) REVERT: G 508 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7017 (mm-30) REVERT: G 537 ASN cc_start: 0.8403 (t0) cc_final: 0.8080 (t0) REVERT: G 886 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6938 (mmm) REVERT: K 57 ASP cc_start: 0.8244 (t0) cc_final: 0.8003 (t0) REVERT: J 72 MET cc_start: 0.5474 (tpt) cc_final: 0.3489 (ttm) REVERT: J 134 PHE cc_start: 0.7088 (t80) cc_final: 0.6845 (t80) REVERT: H 310 LEU cc_start: 0.5952 (mt) cc_final: 0.5547 (mt) REVERT: H 311 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6153 (mp) REVERT: M 75 PHE cc_start: 0.6430 (m-80) cc_final: 0.6116 (m-80) REVERT: M 151 TYR cc_start: 0.2716 (t80) cc_final: 0.1674 (t80) REVERT: M 211 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.3875 (pp) REVERT: M 374 MET cc_start: 0.4655 (pmm) cc_final: 0.3914 (pmm) REVERT: M 460 MET cc_start: -0.0346 (ptt) cc_final: -0.0599 (ttt) REVERT: M 462 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6624 (tp) REVERT: M 475 LEU cc_start: 0.6983 (pp) cc_final: 0.5964 (tp) REVERT: L 22 ARG cc_start: 0.5422 (mmm160) cc_final: 0.4846 (mmm160) REVERT: L 73 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5897 (m-10) REVERT: L 82 ASP cc_start: -0.0744 (t70) cc_final: -0.0958 (t0) REVERT: L 214 MET cc_start: 0.2882 (tmm) cc_final: 0.2329 (tmm) REVERT: L 313 MET cc_start: 0.4302 (mtp) cc_final: 0.3978 (mtt) REVERT: L 592 ARG cc_start: 0.4289 (mtt90) cc_final: 0.3204 (ttp80) REVERT: N 42 VAL cc_start: 0.6742 (p) cc_final: 0.6339 (m) REVERT: N 68 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5918 (tpt-90) REVERT: N 140 PHE cc_start: 0.5142 (m-80) cc_final: 0.4766 (m-80) REVERT: N 151 ARG cc_start: 0.5657 (ptp-170) cc_final: 0.5041 (ttp-110) REVERT: N 286 LEU cc_start: 0.7550 (mp) cc_final: 0.7245 (mp) REVERT: N 321 MET cc_start: 0.3849 (pmm) cc_final: 0.3407 (pmm) REVERT: N 379 MET cc_start: 0.6384 (mmt) cc_final: 0.5394 (mmt) REVERT: N 392 PHE cc_start: 0.6618 (t80) cc_final: 0.6388 (t80) REVERT: N 427 ARG cc_start: 0.6595 (mmm160) cc_final: 0.6213 (mmm160) outliers start: 132 outliers final: 108 residues processed: 1081 average time/residue: 0.4950 time to fit residues: 860.4513 Evaluate side-chains 1137 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1019 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 344 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain G residue 591 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 726 GLN Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 788 THR Chi-restraints excluded: chain G residue 804 GLN Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 843 ASN Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 871 VAL Chi-restraints excluded: chain G residue 886 MET Chi-restraints excluded: chain G residue 900 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 224 HIS Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 475 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 chunk 110 optimal weight: 0.0170 chunk 333 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 372 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN D 150 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 216 ASN ** G 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 766 ASN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.236532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.190127 restraints weight = 53766.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.193946 restraints weight = 74661.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.192153 restraints weight = 32592.528| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 36088 Z= 0.355 Angle : 0.797 14.162 49115 Z= 0.403 Chirality : 0.050 0.312 5554 Planarity : 0.006 0.077 6255 Dihedral : 5.858 163.925 4984 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.11 % Allowed : 28.37 % Favored : 67.52 % 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: -0.59 (0.12), residues: 4573 helix: 0.48 (0.11), residues: 2459 sheet: -1.14 (0.30), residues: 304 loop : -1.41 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 94 HIS 0.015 0.002 HIS G 653 PHE 0.058 0.002 PHE H 282 TYR 0.026 0.002 TYR M 435 ARG 0.013 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12602.36 seconds wall clock time: 235 minutes 1.58 seconds (14101.58 seconds total)