Starting phenix.real_space_refine on Sun Jul 5 14:05:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.map" model { file = "/net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dei_46791/07_2026/9dei_46791.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.084 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 Zn 5 6.06 5 P 77 5.49 5 Mg 3 5.21 5 S 150 5.16 5 C 17179 2.51 5 N 4940 2.21 5 O 5766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28120 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2991 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 351} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2466 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain breaks: 1 Chain: "C" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4135 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 33, 'TRANS': 487} Chain breaks: 2 Chain: "D" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 1 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "F" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1040 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "G" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1195 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "I" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain breaks: 2 Chain: "J" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Chain: "K" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1393 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1141 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 1 Chain: "M" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1034 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1148 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 131} Chain: "O" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1545 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain breaks: 3 Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "R" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1621 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 61} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'5GP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "N" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3429 SG CYS B 123 139.889 125.016 31.534 1.00 22.01 S ATOM 3453 SG CYS B 126 138.151 122.522 33.860 1.00 25.22 S ATOM 5827 SG CYS C 148 86.491 125.967 42.681 1.00 4.18 S ATOM 5852 SG CYS C 151 90.156 126.756 43.765 1.00 2.61 S ATOM 9657 SG CYS D 51 141.942 127.699 98.387 1.00 10.22 S ATOM 9679 SG CYS D 54 141.022 124.276 96.762 1.00 6.78 S ATOM 18987 SG CYS K 410 179.624 71.526 37.044 1.00 16.86 S ATOM 19007 SG CYS K 413 175.970 70.095 37.173 1.00 18.98 S ATOM 23743 SG CYS O 499 127.773 116.278 108.044 1.00 45.50 S ATOM 23764 SG CYS O 502 128.399 117.131 111.670 1.00 54.48 S Time building chain proxies: 5.88, per 1000 atoms: 0.21 Number of scatterers: 28120 At special positions: 0 Unit cell: (223.3, 199.1, 147.4, 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) Zn 5 29.99 S 150 16.00 P 77 15.00 Mg 3 11.99 O 5766 8.00 N 4940 7.00 C 17179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 143 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 137 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 123 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 126 " pdb=" ZN C 904 " pdb="ZN ZN C 904 " - pdb=" ND1 HIS C 174 " pdb="ZN ZN C 904 " - pdb=" NE2 HIS C 162 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 151 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 148 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 64 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 70 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 54 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 51 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 426 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 431 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 413 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 410 " pdb=" ZN O 801 " pdb="ZN ZN O 801 " - pdb=" NE2 HIS O 542 " pdb="ZN ZN O 801 " - pdb=" NE2 HIS O 537 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 499 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 502 " Number of angles added : 9 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6228 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 39.5% alpha, 13.3% beta 22 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 53 through 60 removed outlier: 4.520A pdb=" N ALA A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.716A pdb=" N HIS A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 137 Processing helix chain 'A' and resid 141 through 154 Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.692A pdb=" N ALA A 169 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 171 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.665A pdb=" N ARG A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 258 Proline residue: A 239 - end of helix removed outlier: 3.830A pdb=" N LEU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.674A pdb=" N GLN A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.882A pdb=" N LEU A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 270' Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.544A pdb=" N LEU A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.517A pdb=" N GLU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG A 334 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'B' and resid 54 through 65 removed outlier: 4.070A pdb=" N ARG B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.788A pdb=" N GLY B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 155 Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.650A pdb=" N ALA B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.532A pdb=" N LEU B 189 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 190 " --> pdb=" O ASP B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 190' Processing helix chain 'B' and resid 191 through 208 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 228 through 236 removed outlier: 4.139A pdb=" N ARG B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.856A pdb=" N ILE B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 292 through 309 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 317 through 354 removed outlier: 3.590A pdb=" N LYS B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 173 through 190 removed outlier: 3.658A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 180 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 223 through 242 Processing helix chain 'C' and resid 245 through 249 removed outlier: 3.647A pdb=" N LEU C 248 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 280 Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.762A pdb=" N ARG C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 302 removed outlier: 6.126A pdb=" N TRP C 299 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.653A pdb=" N GLU C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 4.168A pdb=" N LEU C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 removed outlier: 4.170A pdb=" N LEU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 334' Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.630A pdb=" N LEU C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 367 Processing helix chain 'C' and resid 383 through 427 removed outlier: 3.704A pdb=" N LEU C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.654A pdb=" N SER C 447 " --> pdb=" O GLY C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 507 through 517 Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.793A pdb=" N LEU C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 Processing helix chain 'C' and resid 584 through 592 Processing helix chain 'C' and resid 594 through 598 removed outlier: 3.618A pdb=" N PHE C 597 " --> pdb=" O ASP C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 654 removed outlier: 4.490A pdb=" N ILE C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 82 through 97 removed outlier: 3.606A pdb=" N HIS D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 129 removed outlier: 4.265A pdb=" N VAL D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 179 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 196 through 207 Processing helix chain 'D' and resid 209 through 218 removed outlier: 3.701A pdb=" N VAL D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 Processing helix chain 'D' and resid 266 through 303 removed outlier: 3.924A pdb=" N ILE D 287 " --> pdb=" O MET D 283 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 319 removed outlier: 4.561A pdb=" N LYS D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.648A pdb=" N LEU D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 removed outlier: 4.052A pdb=" N ASP D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 383 " --> pdb=" O TRP D 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 285 through 288 Processing helix chain 'F' and resid 339 through 350 Processing helix chain 'G' and resid 419 through 431 Processing helix chain 'G' and resid 533 through 543 Processing helix chain 'H' and resid 76 through 87 Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 39 through 47 removed outlier: 3.724A pdb=" N THR I 43 " --> pdb=" O HIS I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 88 Processing helix chain 'I' and resid 97 through 100 Processing helix chain 'I' and resid 153 through 170 removed outlier: 3.888A pdb=" N GLU I 162 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG I 169 " --> pdb=" O LYS I 165 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 211 Processing helix chain 'J' and resid 76 through 87 Processing helix chain 'K' and resid 419 through 431 Processing helix chain 'K' and resid 461 through 465 Processing helix chain 'K' and resid 532 through 543 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 73 through 80 Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 154 through 169 removed outlier: 3.580A pdb=" N LEU L 158 " --> pdb=" O ARG L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 87 Processing helix chain 'M' and resid 121 through 125 removed outlier: 3.866A pdb=" N GLY M 125 " --> pdb=" O PRO M 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 288 Processing helix chain 'N' and resid 339 through 350 Processing helix chain 'O' and resid 489 through 494 removed outlier: 3.664A pdb=" N ALA O 493 " --> pdb=" O ALA O 489 " (cutoff:3.500A) Processing helix chain 'O' and resid 499 through 513 Processing helix chain 'O' and resid 530 through 542 Processing helix chain 'O' and resid 547 through 560 removed outlier: 3.685A pdb=" N GLN O 560 " --> pdb=" O ALA O 556 " (cutoff:3.500A) Processing helix chain 'O' and resid 710 through 716 removed outlier: 4.059A pdb=" N LEU O 714 " --> pdb=" O PRO O 710 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS O 715 " --> pdb=" O ALA O 711 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.731A pdb=" N THR A 107 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.521A pdb=" N ARG A 325 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.650A pdb=" N GLU B 128 " --> pdb=" O CYS B 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.522A pdb=" N GLU C 153 " --> pdb=" O CYS C 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 451 through 454 removed outlier: 8.656A pdb=" N VAL N 255 " --> pdb=" O GLU C 459 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG C 461 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 529 through 531 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 529 through 531 current: chain 'M' and resid 42 through 55 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 63 through 75 current: chain 'M' and resid 117 through 120 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 117 through 120 current: chain 'N' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 330 through 337 current: chain 'N' and resid 374 through 383 Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.774A pdb=" N HIS D 49 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 56 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 138 through 141 Processing sheet with id=AB1, first strand: chain 'E' and resid 22 through 39 removed outlier: 16.688A pdb=" N LEU E 27 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 15.803A pdb=" N ILE E 54 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY E 29 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR E 52 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL E 31 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR E 50 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP E 33 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 48 " --> pdb=" O ASP E 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 75 current: chain 'E' and resid 112 through 120 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 112 through 120 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 337 current: chain 'F' and resid 374 through 383 Processing sheet with id=AB2, first strand: chain 'G' and resid 408 through 409 Processing sheet with id=AB3, first strand: chain 'G' and resid 488 through 489 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 488 through 489 current: chain 'G' and resid 509 through 516 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 525 through 532 current: chain 'G' and resid 567 through 576 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 567 through 576 current: chain 'H' and resid 42 through 55 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 64 through 75 current: chain 'H' and resid 117 through 120 Processing sheet with id=AB4, first strand: chain 'H' and resid 103 through 105 Processing sheet with id=AB5, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'I' and resid 102 through 118 removed outlier: 9.098A pdb=" N GLY I 108 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N GLU I 131 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL I 110 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU I 129 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN I 112 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE I 127 " --> pdb=" O GLN I 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 141 through 149 current: chain 'I' and resid 194 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 201 current: chain 'J' and resid 42 through 55 removed outlier: 3.753A pdb=" N THR J 51 " --> pdb=" O ASP J 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 64 through 75 current: chain 'J' and resid 117 through 120 Processing sheet with id=AB7, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'K' and resid 408 through 409 Processing sheet with id=AB9, first strand: chain 'K' and resid 493 through 503 removed outlier: 6.910A pdb=" N THR K 513 " --> pdb=" O LEU K 500 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL K 502 " --> pdb=" O HIS K 511 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS K 511 " --> pdb=" O VAL K 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 525 through 531 current: chain 'K' and resid 567 through 576 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 567 through 576 current: chain 'L' and resid 34 through 46 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 81 through 92 current: chain 'L' and resid 126 through 136 Processing sheet with id=AC1, first strand: chain 'M' and resid 103 through 106 removed outlier: 3.529A pdb=" N LYS M 111 " --> pdb=" O GLU M 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 140 through 141 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 140 through 141 current: chain 'O' and resid 646 through 656 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 697 through 705 current: chain 'O' and resid 748 through 751 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 748 through 751 current: chain 'P' and resid 42 through 55 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 64 through 75 current: chain 'P' and resid 117 through 120 Processing sheet with id=AC3, first strand: chain 'M' and resid 146 through 147 removed outlier: 6.599A pdb=" N GLU M 146 " --> pdb=" O VAL O 736 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 281 through 283 Processing sheet with id=AC5, first strand: chain 'O' and resid 497 through 498 Processing sheet with id=AC6, first strand: chain 'P' and resid 103 through 106 removed outlier: 3.531A pdb=" N LYS P 111 " --> pdb=" O GLU P 106 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4446 1.31 - 1.44: 7960 1.44 - 1.57: 15719 1.57 - 1.69: 154 1.69 - 1.82: 218 Bond restraints: 28497 Sorted by residual: bond pdb=" C3' 5GP R 101 " pdb=" O3' 5GP R 101 " ideal model delta sigma weight residual 1.414 1.188 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C6 5GP R 101 " pdb=" O6 5GP R 101 " ideal model delta sigma weight residual 1.232 1.400 -0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" C2 5GP R 101 " pdb=" N2 5GP R 101 " ideal model delta sigma weight residual 1.335 1.459 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" O3P 5GP R 101 " pdb=" P 5GP R 101 " ideal model delta sigma weight residual 1.536 1.653 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C5 5GP R 101 " pdb=" N7 5GP R 101 " ideal model delta sigma weight residual 1.387 1.495 -0.108 2.00e-02 2.50e+03 2.89e+01 ... (remaining 28492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 38774 2.86 - 5.71: 226 5.71 - 8.57: 21 8.57 - 11.42: 5 11.42 - 14.28: 1 Bond angle restraints: 39027 Sorted by residual: angle pdb=" C1' U R 20 " pdb=" N1 U R 20 " pdb=" C2 U R 20 " ideal model delta sigma weight residual 117.70 125.98 -8.28 1.20e+00 6.94e-01 4.77e+01 angle pdb=" N1 U R 20 " pdb=" C2 U R 20 " pdb=" O2 U R 20 " ideal model delta sigma weight residual 122.80 127.42 -4.62 7.00e-01 2.04e+00 4.36e+01 angle pdb=" O2 U R 20 " pdb=" C2 U R 20 " pdb=" N3 U R 20 " ideal model delta sigma weight residual 122.20 117.87 4.33 7.00e-01 2.04e+00 3.82e+01 angle pdb=" C ALA I 96 " pdb=" CA ALA I 96 " pdb=" CB ALA I 96 " ideal model delta sigma weight residual 116.63 110.28 6.35 1.16e+00 7.43e-01 3.00e+01 angle pdb=" C1' G R 16 " pdb=" N9 G R 16 " pdb=" C4 G R 16 " ideal model delta sigma weight residual 126.50 133.52 -7.02 1.30e+00 5.92e-01 2.92e+01 ... (remaining 39022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 16725 33.17 - 66.34: 545 66.34 - 99.51: 67 99.51 - 132.68: 0 132.68 - 165.85: 2 Dihedral angle restraints: 17339 sinusoidal: 7747 harmonic: 9592 Sorted by residual: dihedral pdb=" O4' C R 76 " pdb=" C1' C R 76 " pdb=" N1 C R 76 " pdb=" C2 C R 76 " ideal model delta sinusoidal sigma weight residual 232.00 66.15 165.85 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" O4' U R 20 " pdb=" C1' U R 20 " pdb=" N1 U R 20 " pdb=" C2 U R 20 " ideal model delta sinusoidal sigma weight residual 232.00 135.23 96.77 1 1.70e+01 3.46e-03 3.71e+01 dihedral pdb=" CA HIS H 131 " pdb=" C HIS H 131 " pdb=" N GLY H 132 " pdb=" CA GLY H 132 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 17336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3879 0.063 - 0.126: 571 0.126 - 0.190: 29 0.190 - 0.253: 2 0.253 - 0.316: 2 Chirality restraints: 4483 Sorted by residual: chirality pdb=" C3' 5GP R 101 " pdb=" C2' 5GP R 101 " pdb=" C4' 5GP R 101 " pdb=" O3' 5GP R 101 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1' U R 28 " pdb=" O4' U R 28 " pdb=" C2' U R 28 " pdb=" N1 U R 28 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' 5GP R 101 " pdb=" C1' 5GP R 101 " pdb=" C3' 5GP R 101 " pdb=" O2' 5GP R 101 " both_signs ideal model delta sigma weight residual False -2.81 -2.58 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 4480 not shown) Planarity restraints: 4765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 6 " -0.035 2.00e-02 2.50e+03 1.44e-02 6.20e+00 pdb=" N9 G R 6 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G R 6 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G R 6 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G R 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G R 6 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G R 6 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G R 6 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G R 6 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 6 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G R 6 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G R 6 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 28 " 0.024 2.00e-02 2.50e+03 1.26e-02 3.58e+00 pdb=" N1 U R 28 " -0.028 2.00e-02 2.50e+03 pdb=" C2 U R 28 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U R 28 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U R 28 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U R 28 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U R 28 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U R 28 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U R 28 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 232 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR D 232 " -0.032 2.00e-02 2.50e+03 pdb=" O THR D 232 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE D 233 " 0.011 2.00e-02 2.50e+03 ... (remaining 4762 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.20: 23741 3.20 - 3.76: 41718 3.76 - 4.33: 57891 4.33 - 4.90: 95458 Nonbonded interactions: 219100 Sorted by model distance: nonbonded pdb=" OE1 GLU C 353 " pdb="MG MG C 902 " model vdw 2.061 2.170 nonbonded pdb=" OE2 GLU C 353 " pdb="MG MG C 903 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP C 279 " pdb="MG MG C 903 " model vdw 2.131 2.170 nonbonded pdb=" OG SER N 324 " pdb=" OD2 ASP N 327 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR L 96 " pdb=" OE1 GLU L 169 " model vdw 2.190 3.040 ... (remaining 219095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'H' and resid 20 through 133) selection = (chain 'J' and resid 20 through 133) selection = (chain 'M' and resid 20 through 133) selection = (chain 'P' and resid 20 through 133) } ncs_group { reference = chain 'F' selection = (chain 'N' and resid 265 through 393) } ncs_group { reference = chain 'G' selection = (chain 'K' and (resid 406 through 438 or resid 462 through 587)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.060 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.004 0.226 28518 Z= 0.187 Angle : 0.609 14.280 39036 Z= 0.357 Chirality : 0.043 0.316 4483 Planarity : 0.004 0.042 4765 Dihedral : 15.602 165.851 11111 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 0.69 % Allowed : 6.95 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3251 helix: 1.68 (0.16), residues: 1130 sheet: 1.22 (0.17), residues: 795 loop : -0.64 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 235 TYR 0.016 0.001 TYR M 40 PHE 0.014 0.001 PHE A 31 TRP 0.020 0.002 TRP B 287 HIS 0.009 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 (28497) covalent geometry : angle 0.60298 / 0.36 (39027) hydrogen bonds : bond 0.16794 / 11.05 ( 1071) hydrogen bonds : angle 5.39839 / 3.91 ( 2986) metal coordination : bond 0.01441 / 0.61 ( 20) metal coordination : angle 5.45311 / 2.36 ( 9) Misc. bond : bond 0.00081 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 535 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8327 (mtp) cc_final: 0.8043 (mtp) REVERT: B 277 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7514 (mtm-85) REVERT: C 168 ARG cc_start: 0.5868 (ptm-80) cc_final: 0.3914 (ttt90) REVERT: C 290 MET cc_start: 0.8343 (ptm) cc_final: 0.8016 (ptp) REVERT: N 349 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6733 (tt0) REVERT: P 50 THR cc_start: 0.8341 (t) cc_final: 0.7980 (m) REVERT: P 100 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8392 (mmm160) outliers start: 20 outliers final: 17 residues processed: 553 average time/residue: 0.7028 time to fit residues: 444.7440 Evaluate side-chains 347 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.0370 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 215 ASN B 111 ASN B 113 GLN D 272 GLN E 85 GLN E 96 ASN E 104 GLN E 131 HIS F 300 ASN G 565 ASN H 124 HIS ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 HIS ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 546 ASN M 23 ASN M 142 ASN P 23 ASN P 104 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.183798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156274 restraints weight = 34475.422| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.67 r_work: 0.3611 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28518 Z= 0.174 Angle : 0.661 12.974 39036 Z= 0.355 Chirality : 0.046 0.414 4483 Planarity : 0.005 0.073 4765 Dihedral : 13.443 170.993 4855 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 3.79 % Allowed : 13.21 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3251 helix: 1.65 (0.15), residues: 1145 sheet: 1.09 (0.18), residues: 779 loop : -0.85 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 498 TYR 0.026 0.002 TYR K 568 PHE 0.029 0.002 PHE L 39 TRP 0.034 0.002 TRP I 163 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (28497) covalent geometry : angle 0.65640 / 0.35 (39027) hydrogen bonds : bond 0.07551 / 5.12 ( 1071) hydrogen bonds : angle 4.51151 / 3.28 ( 2986) metal coordination : bond 0.01429 / 0.68 ( 20) metal coordination : angle 5.02277 / 2.76 ( 9) Misc. bond : bond 0.00344 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 342 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8125 (mtp) cc_final: 0.7808 (mtp) REVERT: C 168 ARG cc_start: 0.5873 (ptm-80) cc_final: 0.4055 (tpt-90) REVERT: C 602 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.6776 (p) REVERT: E 118 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8598 (mp) REVERT: I 83 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6028 (mt0) REVERT: J 106 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5121 (mm-30) REVERT: L 31 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.4036 (pt) REVERT: N 294 MET cc_start: 0.8331 (mmt) cc_final: 0.7356 (mmt) REVERT: N 349 GLN cc_start: 0.7611 (tp-100) cc_final: 0.6918 (tt0) REVERT: N 392 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8061 (tttm) REVERT: O 631 MET cc_start: 0.8291 (mmt) cc_final: 0.7235 (mmt) REVERT: O 732 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: P 50 THR cc_start: 0.8656 (t) cc_final: 0.8299 (m) REVERT: P 100 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8619 (mmm160) outliers start: 110 outliers final: 46 residues processed: 418 average time/residue: 0.6564 time to fit residues: 317.2911 Evaluate side-chains 363 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain K residue 466 SER Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain O residue 732 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 14 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 204 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 308 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 215 ASN B 113 GLN E 131 HIS I 105 HIS I 158 ASN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 511 HIS M 61 GLN M 142 ASN P 104 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.186206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147082 restraints weight = 34802.412| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.98 r_work: 0.3299 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28518 Z= 0.124 Angle : 0.578 11.083 39036 Z= 0.309 Chirality : 0.043 0.435 4483 Planarity : 0.004 0.063 4765 Dihedral : 13.277 174.823 4850 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 3.06 % Allowed : 15.00 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3251 helix: 1.81 (0.15), residues: 1158 sheet: 1.14 (0.18), residues: 780 loop : -0.87 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 159 TYR 0.022 0.001 TYR I 195 PHE 0.017 0.001 PHE J 79 TRP 0.059 0.002 TRP I 163 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (28497) covalent geometry : angle 0.57572 / 0.31 (39027) hydrogen bonds : bond 0.06084 / 4.15 ( 1071) hydrogen bonds : angle 4.26916 / 3.10 ( 2986) metal coordination : bond 0.01214 / 0.58 ( 20) metal coordination : angle 3.38824 / 1.82 ( 9) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 328 time to evaluate : 0.824 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: A 212 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6079 (ptm-80) REVERT: A 365 GLN cc_start: 0.7487 (mp10) cc_final: 0.7218 (mp10) REVERT: B 235 MET cc_start: 0.8086 (mtp) cc_final: 0.7770 (mtp) REVERT: C 120 GLU cc_start: 0.6602 (pt0) cc_final: 0.6183 (tt0) REVERT: C 168 ARG cc_start: 0.5454 (ptm160) cc_final: 0.3143 (tpt-90) REVERT: C 290 MET cc_start: 0.8247 (ptm) cc_final: 0.7856 (ptp) REVERT: C 292 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8770 (mp) REVERT: D 85 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6784 (mmp80) REVERT: D 123 MET cc_start: 0.8060 (mtp) cc_final: 0.7320 (mtp) REVERT: H 25 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8455 (t) REVERT: I 160 MET cc_start: 0.4349 (pp-130) cc_final: 0.3911 (pp-130) REVERT: K 494 THR cc_start: 0.7942 (p) cc_final: 0.7639 (t) REVERT: N 294 MET cc_start: 0.8231 (mmt) cc_final: 0.7359 (mmt) REVERT: N 349 GLN cc_start: 0.8076 (tp-100) cc_final: 0.6805 (tt0) REVERT: N 392 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8105 (tttm) REVERT: O 536 ASP cc_start: 0.8127 (m-30) cc_final: 0.7913 (m-30) REVERT: P 50 THR cc_start: 0.8724 (t) cc_final: 0.8386 (m) outliers start: 89 outliers final: 43 residues processed: 391 average time/residue: 0.6302 time to fit residues: 285.4543 Evaluate side-chains 346 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 131 HIS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 159 ARG Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 227 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 257 ASN B 113 GLN E 58 HIS E 69 HIS E 131 HIS H 112 HIS I 158 ASN J 70 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN M 142 ASN P 104 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.179319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147932 restraints weight = 34188.370| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.81 r_work: 0.3505 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28518 Z= 0.243 Angle : 0.735 10.567 39036 Z= 0.391 Chirality : 0.050 0.358 4483 Planarity : 0.006 0.070 4765 Dihedral : 13.488 169.978 4845 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 4.40 % Allowed : 15.11 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3251 helix: 1.37 (0.15), residues: 1154 sheet: 0.77 (0.18), residues: 772 loop : -1.09 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 334 TYR 0.025 0.003 TYR C 301 PHE 0.024 0.003 PHE P 47 TRP 0.065 0.003 TRP I 163 HIS 0.010 0.002 HIS H 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (28497) covalent geometry : angle 0.72906 / 0.39 (39027) hydrogen bonds : bond 0.08917 / 6.08 ( 1071) hydrogen bonds : angle 4.46280 / 3.25 ( 2986) metal coordination : bond 0.01978 / 1.00 ( 20) metal coordination : angle 6.39963 / 3.74 ( 9) Misc. bond : bond 0.00223 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 313 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8941 (mtm) cc_final: 0.8257 (mtm) REVERT: A 212 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6282 (ptm-80) REVERT: A 368 ASP cc_start: 0.8024 (t0) cc_final: 0.7662 (t0) REVERT: B 167 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7661 (mtm-85) REVERT: C 168 ARG cc_start: 0.5980 (ptm160) cc_final: 0.4080 (tpt-90) REVERT: C 534 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: D 85 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7367 (mmp80) REVERT: D 203 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: D 209 MET cc_start: 0.8646 (mtp) cc_final: 0.8274 (mtp) REVERT: E 85 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: E 118 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8671 (mp) REVERT: G 425 MET cc_start: -0.2837 (tmt) cc_final: -0.5695 (pp-130) REVERT: I 83 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.5925 (mt0) REVERT: N 294 MET cc_start: 0.8402 (mmt) cc_final: 0.7670 (mmt) REVERT: N 392 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8286 (tttm) REVERT: P 50 THR cc_start: 0.8806 (t) cc_final: 0.8358 (m) REVERT: P 86 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7951 (mtmm) outliers start: 128 outliers final: 63 residues processed: 398 average time/residue: 0.6416 time to fit residues: 295.2618 Evaluate side-chains 370 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 297 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 534 GLN Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 112 HIS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 578 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain O residue 732 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 138 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN I 157 GLN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 ASN M 142 ASN P 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154966 restraints weight = 34309.286| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.70 r_work: 0.3597 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28518 Z= 0.140 Angle : 0.602 10.010 39036 Z= 0.323 Chirality : 0.044 0.342 4483 Planarity : 0.005 0.100 4765 Dihedral : 13.401 172.462 4845 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 3.54 % Allowed : 16.90 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3251 helix: 1.67 (0.15), residues: 1148 sheet: 0.78 (0.18), residues: 773 loop : -1.11 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 98 TYR 0.021 0.001 TYR C 431 PHE 0.019 0.002 PHE I 93 TRP 0.070 0.002 TRP I 163 HIS 0.012 0.001 HIS H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (28497) covalent geometry : angle 0.59834 / 0.32 (39027) hydrogen bonds : bond 0.06969 / 4.75 ( 1071) hydrogen bonds : angle 4.28332 / 3.11 ( 2986) metal coordination : bond 0.01402 / 0.67 ( 20) metal coordination : angle 4.45028 / 2.53 ( 9) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 309 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8926 (mtm) cc_final: 0.8269 (mtm) REVERT: A 212 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6196 (ptm-80) REVERT: C 120 GLU cc_start: 0.6770 (pt0) cc_final: 0.6537 (tt0) REVERT: C 168 ARG cc_start: 0.6054 (ptm160) cc_final: 0.4170 (tpt-90) REVERT: C 292 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (mp) REVERT: D 85 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7170 (mmp80) REVERT: D 203 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: D 259 ASP cc_start: 0.7330 (t0) cc_final: 0.7123 (t0) REVERT: D 285 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7935 (m-40) REVERT: E 118 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8599 (mp) REVERT: G 425 MET cc_start: -0.2652 (tmt) cc_final: -0.5594 (pp-130) REVERT: H 98 ARG cc_start: 0.8256 (ttm110) cc_final: 0.8039 (ttm110) REVERT: I 13 ASP cc_start: 0.7613 (m-30) cc_final: 0.7349 (m-30) REVERT: N 294 MET cc_start: 0.8304 (mmt) cc_final: 0.7472 (mmt) REVERT: N 392 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8158 (tttm) REVERT: P 50 THR cc_start: 0.8742 (t) cc_final: 0.8378 (m) outliers start: 103 outliers final: 61 residues processed: 381 average time/residue: 0.6526 time to fit residues: 289.0192 Evaluate side-chains 356 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 578 MET Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain O residue 732 MET Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 HIS B 113 GLN D 369 GLN G 537 GLN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN P 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.178739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150808 restraints weight = 34008.354| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.73 r_work: 0.3539 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 28518 Z= 0.239 Angle : 0.730 10.706 39036 Z= 0.390 Chirality : 0.050 0.336 4483 Planarity : 0.006 0.085 4765 Dihedral : 13.561 169.650 4845 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 4.51 % Allowed : 16.48 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3251 helix: 1.27 (0.15), residues: 1149 sheet: 0.50 (0.18), residues: 786 loop : -1.29 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 159 TYR 0.021 0.002 TYR C 301 PHE 0.022 0.002 PHE M 47 TRP 0.080 0.003 TRP I 163 HIS 0.011 0.002 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (28497) covalent geometry : angle 0.72405 / 0.39 (39027) hydrogen bonds : bond 0.08898 / 6.06 ( 1071) hydrogen bonds : angle 4.45993 / 3.23 ( 2986) metal coordination : bond 0.01920 / 0.97 ( 20) metal coordination : angle 6.21054 / 3.54 ( 9) Misc. bond : bond 0.00144 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 311 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8892 (mtm) cc_final: 0.8314 (mtm) REVERT: A 212 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6570 (ptm-80) REVERT: B 167 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7534 (mtm-85) REVERT: C 104 TYR cc_start: 0.4372 (OUTLIER) cc_final: 0.3086 (t80) REVERT: C 168 ARG cc_start: 0.6036 (ptm160) cc_final: 0.4049 (tpt170) REVERT: C 292 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8837 (mp) REVERT: D 85 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7337 (mmp80) REVERT: D 203 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: D 209 MET cc_start: 0.8615 (mtp) cc_final: 0.8231 (mtp) REVERT: E 118 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8655 (mp) REVERT: G 425 MET cc_start: -0.2663 (tmt) cc_final: -0.5705 (pp-130) REVERT: G 525 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: G 562 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: N 294 MET cc_start: 0.8445 (mmt) cc_final: 0.7739 (mmt) REVERT: N 392 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8319 (tttm) REVERT: O 705 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: P 50 THR cc_start: 0.8784 (t) cc_final: 0.8304 (m) REVERT: P 85 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7841 (mt0) outliers start: 131 outliers final: 80 residues processed: 403 average time/residue: 0.6900 time to fit residues: 322.0840 Evaluate side-chains 383 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 534 GLN Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 578 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain O residue 705 MET Chi-restraints excluded: chain O residue 732 MET Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 85 GLN Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 316 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 293 optimal weight: 0.0470 chunk 7 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN G 537 GLN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.183736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154229 restraints weight = 34215.107| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.70 r_work: 0.3587 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28518 Z= 0.129 Angle : 0.587 11.388 39036 Z= 0.313 Chirality : 0.043 0.315 4483 Planarity : 0.005 0.067 4765 Dihedral : 13.416 173.764 4845 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 3.44 % Allowed : 17.89 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3251 helix: 1.70 (0.16), residues: 1146 sheet: 0.74 (0.18), residues: 761 loop : -1.14 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 98 TYR 0.021 0.001 TYR C 431 PHE 0.015 0.001 PHE I 93 TRP 0.080 0.002 TRP I 163 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (28497) covalent geometry : angle 0.58440 / 0.31 (39027) hydrogen bonds : bond 0.06347 / 4.32 ( 1071) hydrogen bonds : angle 4.22099 / 3.04 ( 2986) metal coordination : bond 0.01233 / 0.57 ( 20) metal coordination : angle 3.93241 / 2.16 ( 9) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 311 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8917 (mtm) cc_final: 0.8319 (mtm) REVERT: C 104 TYR cc_start: 0.4333 (OUTLIER) cc_final: 0.3049 (t80) REVERT: C 168 ARG cc_start: 0.6059 (ptm160) cc_final: 0.4177 (tpt170) REVERT: C 292 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 85 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7098 (mmp80) REVERT: D 203 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: E 118 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8586 (mp) REVERT: G 425 MET cc_start: -0.2970 (tmt) cc_final: -0.5785 (pp-130) REVERT: G 502 VAL cc_start: 0.8933 (t) cc_final: 0.8728 (t) REVERT: H 98 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8072 (ttm110) REVERT: L 84 GLU cc_start: 0.5990 (tp30) cc_final: 0.5549 (tp30) REVERT: N 294 MET cc_start: 0.8312 (mmt) cc_final: 0.7387 (mmt) REVERT: N 392 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8105 (tttm) REVERT: O 705 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7952 (mtt) REVERT: P 50 THR cc_start: 0.8770 (t) cc_final: 0.8390 (m) REVERT: P 85 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7756 (mt0) outliers start: 100 outliers final: 54 residues processed: 380 average time/residue: 0.6861 time to fit residues: 302.5643 Evaluate side-chains 351 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain O residue 705 MET Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 85 GLN Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 223 optimal weight: 4.9990 chunk 106 optimal weight: 0.0010 chunk 189 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN G 566 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150183 restraints weight = 34017.435| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.85 r_work: 0.3533 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28518 Z= 0.183 Angle : 0.653 11.635 39036 Z= 0.346 Chirality : 0.046 0.304 4483 Planarity : 0.005 0.084 4765 Dihedral : 13.474 172.187 4845 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 3.58 % Allowed : 18.03 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3251 helix: 1.53 (0.15), residues: 1152 sheet: 0.59 (0.18), residues: 780 loop : -1.19 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 98 TYR 0.017 0.002 TYR C 431 PHE 0.021 0.002 PHE M 47 TRP 0.085 0.003 TRP I 163 HIS 0.008 0.001 HIS H 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (28497) covalent geometry : angle 0.64812 / 0.35 (39027) hydrogen bonds : bond 0.07664 / 5.22 ( 1071) hydrogen bonds : angle 4.28616 / 3.10 ( 2986) metal coordination : bond 0.01592 / 0.75 ( 20) metal coordination : angle 5.19095 / 2.86 ( 9) Misc. bond : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 305 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8919 (mtm) cc_final: 0.8324 (mtm) REVERT: C 104 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3053 (t80) REVERT: C 168 ARG cc_start: 0.6131 (ptm160) cc_final: 0.4272 (tpt-90) REVERT: C 292 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8802 (mp) REVERT: D 85 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7205 (mmp80) REVERT: D 203 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: E 118 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8661 (mp) REVERT: G 425 MET cc_start: -0.2996 (tmt) cc_final: -0.5828 (pp-130) REVERT: L 84 GLU cc_start: 0.6200 (tp30) cc_final: 0.5465 (tp30) REVERT: N 294 MET cc_start: 0.8488 (mmt) cc_final: 0.7792 (mmt) REVERT: N 392 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8240 (tttm) REVERT: P 50 THR cc_start: 0.8799 (t) cc_final: 0.8380 (m) REVERT: P 85 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: P 104 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7567 (mt0) outliers start: 104 outliers final: 62 residues processed: 378 average time/residue: 0.6379 time to fit residues: 279.7024 Evaluate side-chains 363 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 24 HIS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 85 GLN Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 234 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN G 537 GLN H 58 HIS J 58 HIS ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN M 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149659 restraints weight = 34047.531| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.79 r_work: 0.3532 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28518 Z= 0.156 Angle : 0.630 13.956 39036 Z= 0.333 Chirality : 0.045 0.286 4483 Planarity : 0.005 0.069 4765 Dihedral : 13.439 172.750 4844 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 3.37 % Allowed : 18.55 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3251 helix: 1.59 (0.15), residues: 1151 sheet: 0.68 (0.18), residues: 761 loop : -1.20 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 98 TYR 0.043 0.002 TYR I 195 PHE 0.024 0.002 PHE L 39 TRP 0.074 0.002 TRP I 163 HIS 0.006 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (28497) covalent geometry : angle 0.62657 / 0.33 (39027) hydrogen bonds : bond 0.07120 / 4.84 ( 1071) hydrogen bonds : angle 4.23250 / 3.06 ( 2986) metal coordination : bond 0.01461 / 0.67 ( 20) metal coordination : angle 4.66922 / 2.54 ( 9) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 301 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8919 (mtm) cc_final: 0.8315 (mtm) REVERT: C 104 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.3167 (t80) REVERT: C 168 ARG cc_start: 0.6041 (ptm160) cc_final: 0.4215 (tpt-90) REVERT: C 292 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 85 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7158 (mmp80) REVERT: D 203 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: E 62 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: E 118 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8638 (mp) REVERT: G 425 MET cc_start: -0.3177 (tmt) cc_final: -0.5883 (pp-130) REVERT: H 98 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8119 (ttm110) REVERT: I 13 ASP cc_start: 0.7629 (m-30) cc_final: 0.7393 (m-30) REVERT: L 84 GLU cc_start: 0.6160 (tp30) cc_final: 0.5477 (tp30) REVERT: N 294 MET cc_start: 0.8441 (mmt) cc_final: 0.7682 (mmt) REVERT: N 354 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6206 (mt-10) REVERT: N 392 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8215 (tttm) REVERT: P 50 THR cc_start: 0.8804 (t) cc_final: 0.8398 (m) REVERT: P 85 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: P 104 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7560 (mt0) outliers start: 98 outliers final: 63 residues processed: 371 average time/residue: 0.6855 time to fit residues: 295.5728 Evaluate side-chains 367 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 354 GLU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 85 GLN Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 91 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 307 optimal weight: 0.5980 chunk 101 optimal weight: 0.0000 chunk 238 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN B 156 HIS D 377 HIS G 537 GLN H 58 HIS J 58 HIS ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144438 restraints weight = 34029.427| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.59 r_work: 0.3304 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28518 Z= 0.125 Angle : 0.591 15.214 39036 Z= 0.311 Chirality : 0.043 0.268 4483 Planarity : 0.005 0.064 4765 Dihedral : 13.365 175.835 4844 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 2.58 % Allowed : 19.44 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3251 helix: 1.77 (0.16), residues: 1153 sheet: 0.76 (0.18), residues: 769 loop : -1.12 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 98 TYR 0.016 0.001 TYR C 431 PHE 0.029 0.001 PHE L 39 TRP 0.073 0.002 TRP I 163 HIS 0.008 0.001 HIS J 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (28497) covalent geometry : angle 0.58863 / 0.31 (39027) hydrogen bonds : bond 0.05941 / 4.04 ( 1071) hydrogen bonds : angle 4.12620 / 2.99 ( 2986) metal coordination : bond 0.01152 / 0.51 ( 20) metal coordination : angle 3.52295 / 1.87 ( 9) Misc. bond : bond 0.00012 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8945 (mtm) cc_final: 0.8284 (mtm) REVERT: C 168 ARG cc_start: 0.5660 (ptm160) cc_final: 0.3566 (tpt-90) REVERT: C 268 ARG cc_start: 0.7483 (tpt90) cc_final: 0.7242 (tpp-160) REVERT: C 292 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 85 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6911 (mmp80) REVERT: E 62 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: E 118 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8656 (mp) REVERT: G 425 MET cc_start: -0.4222 (tmt) cc_final: -0.5978 (pp-130) REVERT: H 25 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (t) REVERT: H 98 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8195 (ttm110) REVERT: L 82 ASN cc_start: 0.6860 (t0) cc_final: 0.6625 (t0) REVERT: L 84 GLU cc_start: 0.7222 (tp30) cc_final: 0.5678 (tp30) REVERT: N 294 MET cc_start: 0.8307 (mmt) cc_final: 0.7481 (mmt) REVERT: N 392 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8135 (tttm) REVERT: P 50 THR cc_start: 0.8804 (t) cc_final: 0.8489 (m) REVERT: P 104 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7857 (mt0) outliers start: 75 outliers final: 52 residues processed: 359 average time/residue: 0.6625 time to fit residues: 275.4055 Evaluate side-chains 348 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 271 ASP Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 387 CYS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 392 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 110 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 321 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN D 315 HIS D 377 HIS G 537 GLN H 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152179 restraints weight = 33949.527| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.77 r_work: 0.3563 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28518 Z= 0.130 Angle : 0.601 14.346 39036 Z= 0.315 Chirality : 0.044 0.258 4483 Planarity : 0.005 0.062 4765 Dihedral : 13.355 175.820 4843 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.44 % Allowed : 19.61 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3251 helix: 1.77 (0.16), residues: 1152 sheet: 0.75 (0.18), residues: 758 loop : -1.10 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 98 TYR 0.041 0.001 TYR I 195 PHE 0.021 0.001 PHE L 39 TRP 0.068 0.002 TRP I 163 HIS 0.008 0.001 HIS M 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (28497) covalent geometry : angle 0.59747 / 0.31 (39027) hydrogen bonds : bond 0.06133 / 4.17 ( 1071) hydrogen bonds : angle 4.10439 / 2.97 ( 2986) metal coordination : bond 0.01194 / 0.55 ( 20) metal coordination : angle 4.18796 / 2.08 ( 9) Misc. bond : bond 0.00046 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10024.20 seconds wall clock time: 171 minutes 3.44 seconds (10263.44 seconds total)