Starting phenix.real_space_refine on Fri Feb 6 21:27:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dei_46791/02_2026/9dei_46791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dei_46791/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dei_46791/02_2026/9dei_46791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dei_46791/02_2026/9dei_46791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dei_46791/02_2026/9dei_46791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dei_46791/02_2026/9dei_46791.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 6.84, per 1000 atoms: 0.24 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: 2.55 Conformation dependent library (CDL) restraints added in 909.9 milliseconds 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: 2.84 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: 5.12 Time building geometry restraints manager: 3.07 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=" 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=" O1P 5GP R 101 " pdb=" P 5GP R 101 " pdb=" O2P 5GP R 101 " ideal model delta sigma weight residual 115.68 101.40 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" CA ALA I 96 " pdb=" C ALA I 96 " pdb=" N SER I 97 " ideal model delta sigma weight residual 119.63 116.65 2.98 8.10e-01 1.52e+00 1.35e+01 angle pdb=" C SER C 281 " pdb=" N TRP C 282 " pdb=" CA TRP C 282 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N PRO P 122 " pdb=" CA PRO P 122 " pdb=" C PRO P 122 " ideal model delta sigma weight residual 110.70 115.12 -4.42 1.22e+00 6.72e-01 1.31e+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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.390 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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= 0.181 Angle : 0.609 14.280 39036 Z= 0.323 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 covalent geometry : bond 0.00351 (28497) covalent geometry : angle 0.60295 (39027) hydrogen bonds : bond 0.16794 ( 1071) hydrogen bonds : angle 5.39839 ( 2986) metal coordination : bond 0.01441 ( 20) metal coordination : angle 5.45311 ( 9) Misc. bond : bond 0.00081 ( 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 : 1.075 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: 0.7507 time to fit residues: 472.0529 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 : 0.801 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 112 HIS H 124 HIS ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 511 HIS K 546 ASN M 23 ASN M 142 ASN P 23 ASN P 104 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155798 restraints weight = 34442.213| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.68 r_work: 0.3608 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28518 Z= 0.170 Angle : 0.663 12.871 39036 Z= 0.349 Chirality : 0.046 0.394 4483 Planarity : 0.005 0.070 4765 Dihedral : 13.441 169.097 4855 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 3.85 % Allowed : 13.39 % Favored : 82.76 % 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: 0.79 (0.14), residues: 3251 helix: 1.63 (0.15), residues: 1149 sheet: 1.09 (0.18), residues: 777 loop : -0.83 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 100 TYR 0.021 0.002 TYR K 568 PHE 0.032 0.002 PHE L 39 TRP 0.034 0.003 TRP I 163 HIS 0.008 0.001 HIS J 58 Details of bonding type rmsd covalent geometry : bond 0.00370 (28497) covalent geometry : angle 0.65794 (39027) hydrogen bonds : bond 0.07484 ( 1071) hydrogen bonds : angle 4.43233 ( 2986) metal coordination : bond 0.01746 ( 20) metal coordination : angle 5.26408 ( 9) Misc. bond : bond 0.00025 ( 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 448 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 336 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8113 (mtp) cc_final: 0.7786 (mtp) REVERT: B 331 MET cc_start: 0.8136 (mmt) cc_final: 0.7853 (tpt) REVERT: C 168 ARG cc_start: 0.5898 (ptm160) cc_final: 0.4084 (tpt-90) REVERT: E 118 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8627 (mp) REVERT: I 83 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6022 (mt0) REVERT: J 106 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5174 (mm-30) REVERT: N 294 MET cc_start: 0.8366 (mmt) cc_final: 0.7465 (mmt) REVERT: N 349 GLN cc_start: 0.7713 (tp-100) cc_final: 0.6952 (tt0) REVERT: N 392 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8072 (tttm) REVERT: O 631 MET cc_start: 0.8309 (mmt) cc_final: 0.7194 (mmt) REVERT: P 50 THR cc_start: 0.8681 (t) cc_final: 0.8345 (m) REVERT: P 86 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7916 (mtmm) REVERT: P 100 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8601 (mmm160) outliers start: 112 outliers final: 47 residues processed: 417 average time/residue: 0.6912 time to fit residues: 331.2328 Evaluate side-chains 355 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 212 ARG 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 G residue 570 VAL 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 J residue 51 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 106 GLU 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 43 CYS 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 86 LYS 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: 0.7980 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 0.0670 chunk 152 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN B 113 GLN D 369 GLN E 131 HIS G 565 ASN I 105 HIS I 158 ASN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN P 104 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.183923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152334 restraints weight = 34556.459| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.80 r_work: 0.3578 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28518 Z= 0.133 Angle : 0.591 9.180 39036 Z= 0.311 Chirality : 0.044 0.362 4483 Planarity : 0.005 0.082 4765 Dihedral : 13.309 171.067 4848 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 3.37 % Allowed : 15.18 % Favored : 81.45 % 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: 0.82 (0.15), residues: 3251 helix: 1.73 (0.15), residues: 1161 sheet: 1.08 (0.18), residues: 780 loop : -0.88 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.017 0.001 TYR K 568 PHE 0.017 0.002 PHE P 47 TRP 0.020 0.002 TRP C 282 HIS 0.009 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00271 (28497) covalent geometry : angle 0.58790 (39027) hydrogen bonds : bond 0.06384 ( 1071) hydrogen bonds : angle 4.25248 ( 2986) metal coordination : bond 0.01288 ( 20) metal coordination : angle 3.96603 ( 9) Misc. bond : bond 0.00028 ( 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 422 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 324 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9019 (mtm) cc_final: 0.8229 (mtm) REVERT: A 212 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6241 (ptm-80) REVERT: B 235 MET cc_start: 0.8117 (mtp) cc_final: 0.7788 (mtp) REVERT: C 168 ARG cc_start: 0.6015 (ptm160) cc_final: 0.4014 (tpt-90) REVERT: C 292 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8782 (mp) REVERT: D 85 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7138 (mmp80) REVERT: D 259 ASP cc_start: 0.7311 (t0) cc_final: 0.7057 (t0) REVERT: D 285 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8273 (m-40) REVERT: G 425 MET cc_start: -0.3669 (pp-130) cc_final: -0.3979 (tmt) REVERT: H 25 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8453 (t) REVERT: I 13 ASP cc_start: 0.7671 (m-30) cc_final: 0.7458 (m-30) REVERT: N 294 MET cc_start: 0.8146 (mmt) cc_final: 0.7301 (mmt) REVERT: N 349 GLN cc_start: 0.7808 (tp-100) cc_final: 0.6954 (tt0) REVERT: N 392 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8014 (tttm) REVERT: P 50 THR cc_start: 0.8673 (t) cc_final: 0.8320 (m) REVERT: P 86 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: P 100 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8647 (mmm160) outliers start: 98 outliers final: 51 residues processed: 392 average time/residue: 0.6880 time to fit residues: 310.9642 Evaluate side-chains 354 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 43 VAL 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 379 LEU 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 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 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 63 VAL Chi-restraints excluded: chain E residue 101 LEU 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 F residue 344 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 33 ASP 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 87 VAL Chi-restraints excluded: chain K residue 433 ILE 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 43 CYS 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 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 52 THR Chi-restraints excluded: chain P residue 86 LYS 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: 8.9990 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 106 GLN B 113 GLN D 262 HIS E 58 HIS ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 142 ASN P 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146833 restraints weight = 34174.551| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.96 r_work: 0.3473 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28518 Z= 0.214 Angle : 0.697 10.336 39036 Z= 0.367 Chirality : 0.048 0.360 4483 Planarity : 0.006 0.058 4765 Dihedral : 13.508 168.391 4845 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 4.16 % Allowed : 15.52 % Favored : 80.32 % 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: 0.42 (0.14), residues: 3251 helix: 1.43 (0.15), residues: 1157 sheet: 0.79 (0.18), residues: 776 loop : -1.09 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.021 0.002 TYR C 301 PHE 0.019 0.002 PHE M 47 TRP 0.026 0.003 TRP D 352 HIS 0.010 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00499 (28497) covalent geometry : angle 0.69102 (39027) hydrogen bonds : bond 0.08473 ( 1071) hydrogen bonds : angle 4.40965 ( 2986) metal coordination : bond 0.01969 ( 20) metal coordination : angle 5.99876 ( 9) Misc. bond : bond 0.00131 ( 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 436 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 315 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8989 (mtm) cc_final: 0.8326 (mtm) REVERT: A 212 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6263 (ptm-80) REVERT: B 167 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7655 (mtm-85) REVERT: B 331 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7976 (tpt) REVERT: C 168 ARG cc_start: 0.5964 (ptm160) cc_final: 0.4024 (tpt-90) REVERT: C 534 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: C 543 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7777 (mtm-85) REVERT: D 85 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7369 (mmp80) REVERT: D 203 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: D 209 MET cc_start: 0.8700 (mtp) cc_final: 0.8303 (mtp) REVERT: D 285 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8118 (m-40) REVERT: E 118 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8659 (mp) REVERT: N 294 MET cc_start: 0.8405 (mmt) cc_final: 0.7667 (mmt) REVERT: N 392 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8330 (tttm) REVERT: O 732 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7008 (mtt) REVERT: P 50 THR cc_start: 0.8823 (t) cc_final: 0.8355 (m) REVERT: P 86 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7494 (mtmm) REVERT: P 100 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8690 (mmm160) outliers start: 121 outliers final: 59 residues processed: 397 average time/residue: 0.6622 time to fit residues: 305.3453 Evaluate side-chains 367 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 272 LYS 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 167 ARG Chi-restraints excluded: chain B residue 331 MET 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 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 534 GLN 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 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 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 329 ASP Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain G residue 538 LYS 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 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 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 49 LEU 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: 2.9990 chunk 197 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 277 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN G 537 GLN I 158 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152413 restraints weight = 34249.281| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.72 r_work: 0.3564 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28518 Z= 0.156 Angle : 0.618 10.087 39036 Z= 0.325 Chirality : 0.045 0.337 4483 Planarity : 0.005 0.057 4765 Dihedral : 13.431 169.406 4845 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 4.16 % Allowed : 16.28 % Favored : 79.56 % 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: 0.46 (0.15), residues: 3251 helix: 1.55 (0.15), residues: 1157 sheet: 0.79 (0.18), residues: 778 loop : -1.13 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 98 TYR 0.019 0.002 TYR C 431 PHE 0.032 0.002 PHE L 39 TRP 0.023 0.002 TRP C 282 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd covalent geometry : bond 0.00343 (28497) covalent geometry : angle 0.61400 (39027) hydrogen bonds : bond 0.07130 ( 1071) hydrogen bonds : angle 4.23596 ( 2986) metal coordination : bond 0.01456 ( 20) metal coordination : angle 4.82806 ( 9) Misc. bond : bond 0.00082 ( 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 434 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 313 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8978 (mtm) cc_final: 0.8342 (mtm) REVERT: B 167 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7452 (mtm-85) REVERT: C 168 ARG cc_start: 0.6147 (ptm160) cc_final: 0.4297 (tpt170) REVERT: C 292 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8800 (mp) REVERT: D 85 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7176 (mmp80) REVERT: D 203 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: D 285 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8001 (m-40) REVERT: E 118 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8630 (mp) REVERT: G 425 MET cc_start: -0.2628 (tmt) cc_final: -0.5500 (pp-130) REVERT: N 294 MET cc_start: 0.8408 (mmt) cc_final: 0.7645 (mmt) REVERT: N 392 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8215 (tttm) REVERT: O 732 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7087 (mtt) REVERT: P 50 THR cc_start: 0.8768 (t) cc_final: 0.8384 (m) REVERT: P 85 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: P 86 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7848 (mtmm) REVERT: P 100 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8612 (mmm160) outliers start: 121 outliers final: 71 residues processed: 400 average time/residue: 0.6508 time to fit residues: 301.6070 Evaluate side-chains 371 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 171 VAL 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 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 154 GLU 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 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 493 ILE Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 532 ARG 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 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 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 G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain H residue 24 SER 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 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 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 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 85 GLN Chi-restraints excluded: chain P residue 86 LYS 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: 1.9990 chunk 121 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 305 optimal weight: 0.0870 chunk 184 optimal weight: 0.0970 chunk 234 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 156 HIS D 377 HIS G 537 GLN I 158 ASN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 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 = 0.4172 r_free = 0.4172 target = 0.182156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151351 restraints weight = 34142.727| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.80 r_work: 0.3546 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28518 Z= 0.140 Angle : 0.597 11.232 39036 Z= 0.313 Chirality : 0.044 0.310 4483 Planarity : 0.005 0.061 4765 Dihedral : 13.397 171.043 4845 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 3.96 % Allowed : 16.86 % Favored : 79.18 % 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: 0.54 (0.15), residues: 3251 helix: 1.64 (0.15), residues: 1159 sheet: 0.80 (0.18), residues: 771 loop : -1.10 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 98 TYR 0.026 0.001 TYR I 195 PHE 0.022 0.002 PHE L 37 TRP 0.020 0.002 TRP C 282 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd covalent geometry : bond 0.00300 (28497) covalent geometry : angle 0.59326 (39027) hydrogen bonds : bond 0.06626 ( 1071) hydrogen bonds : angle 4.14157 ( 2986) metal coordination : bond 0.01346 ( 20) metal coordination : angle 4.26223 ( 9) Misc. bond : bond 0.00050 ( 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 421 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 306 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8982 (mtm) cc_final: 0.8346 (mtm) REVERT: B 167 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7464 (mtm-85) REVERT: C 168 ARG cc_start: 0.6013 (ptm160) cc_final: 0.4262 (tpt-90) REVERT: C 292 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8828 (mp) REVERT: D 85 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7169 (mmp80) REVERT: D 203 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: D 259 ASP cc_start: 0.7394 (t0) cc_final: 0.7187 (t0) REVERT: E 118 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8619 (mp) REVERT: G 425 MET cc_start: -0.2814 (tmt) cc_final: -0.5519 (pp-130) REVERT: H 25 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8498 (t) REVERT: H 88 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: H 98 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8188 (ttm110) REVERT: L 84 GLU cc_start: 0.6245 (tp30) cc_final: 0.5512 (tp30) REVERT: N 294 MET cc_start: 0.8389 (mmt) cc_final: 0.7714 (mmt) REVERT: N 392 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8216 (tttm) REVERT: P 50 THR cc_start: 0.8793 (t) cc_final: 0.8410 (m) REVERT: P 86 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (mtmm) outliers start: 115 outliers final: 70 residues processed: 389 average time/residue: 0.6950 time to fit residues: 312.3248 Evaluate side-chains 363 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 43 VAL 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 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 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 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 142 ASP Chi-restraints excluded: chain C residue 154 GLU 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 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 493 ILE Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 534 GLN 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 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 310 LYS 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 58 HIS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 88 LYS 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 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 495 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 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 P residue 49 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 316 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN G 537 GLN J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.182069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152204 restraints weight = 33979.419| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.73 r_work: 0.3566 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28518 Z= 0.144 Angle : 0.604 11.433 39036 Z= 0.316 Chirality : 0.044 0.287 4483 Planarity : 0.005 0.094 4765 Dihedral : 13.397 171.141 4845 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 3.85 % Allowed : 17.38 % Favored : 78.77 % 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: 1.63 (0.15), residues: 1158 sheet: 0.74 (0.18), residues: 774 loop : -1.11 (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 I 93 TRP 0.019 0.002 TRP C 282 HIS 0.007 0.001 HIS M 131 Details of bonding type rmsd covalent geometry : bond 0.00315 (28497) covalent geometry : angle 0.60006 (39027) hydrogen bonds : bond 0.06685 ( 1071) hydrogen bonds : angle 4.12681 ( 2986) metal coordination : bond 0.01145 ( 20) metal coordination : angle 4.46505 ( 9) Misc. bond : bond 0.00069 ( 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 406 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8967 (mtm) cc_final: 0.8312 (mtm) REVERT: B 167 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: B 325 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: C 168 ARG cc_start: 0.6036 (ptm160) cc_final: 0.4323 (tpt-90) REVERT: C 292 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8829 (mp) REVERT: D 85 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7150 (mmp80) REVERT: D 285 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7952 (m-40) REVERT: E 118 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8631 (mp) REVERT: G 425 MET cc_start: -0.3062 (tmt) cc_final: -0.5651 (pp-130) REVERT: H 88 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7810 (mtpp) REVERT: L 84 GLU cc_start: 0.6153 (tp30) cc_final: 0.5327 (tp30) REVERT: M 35 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: N 294 MET cc_start: 0.8389 (mmt) cc_final: 0.7672 (mmt) REVERT: N 392 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8192 (tttm) REVERT: O 705 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: P 50 THR cc_start: 0.8796 (t) cc_final: 0.8394 (m) REVERT: P 86 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7945 (mtmm) REVERT: P 104 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7558 (mt0) outliers start: 112 outliers final: 68 residues processed: 376 average time/residue: 0.7326 time to fit residues: 318.6124 Evaluate side-chains 369 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 289 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 43 VAL 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 283 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LEU 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 B residue 167 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 154 GLU 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 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 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 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 ASN 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 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 24 SER 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 88 LYS 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 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 578 MET Chi-restraints excluded: chain K residue 587 THR Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 35 GLN 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 705 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 104 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: 4.9990 chunk 189 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN C 482 HIS G 537 GLN H 112 HIS J 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN N 299 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146955 restraints weight = 33927.054| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.83 r_work: 0.3481 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 28518 Z= 0.253 Angle : 0.750 12.624 39036 Z= 0.392 Chirality : 0.050 0.281 4483 Planarity : 0.007 0.148 4765 Dihedral : 13.560 167.235 4842 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 4.34 % Allowed : 17.21 % Favored : 78.46 % 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: 0.02 (0.14), residues: 3251 helix: 1.18 (0.15), residues: 1162 sheet: 0.48 (0.18), residues: 776 loop : -1.35 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 334 TYR 0.025 0.003 TYR I 195 PHE 0.033 0.003 PHE L 30 TRP 0.021 0.003 TRP C 282 HIS 0.011 0.002 HIS H 131 Details of bonding type rmsd covalent geometry : bond 0.00605 (28497) covalent geometry : angle 0.74417 (39027) hydrogen bonds : bond 0.09116 ( 1071) hydrogen bonds : angle 4.40565 ( 2986) metal coordination : bond 0.02273 ( 20) metal coordination : angle 6.43071 ( 9) Misc. bond : bond 0.00178 ( 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 432 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 306 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8911 (mtm) cc_final: 0.8337 (mtm) REVERT: B 167 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: C 168 ARG cc_start: 0.6156 (ptm160) cc_final: 0.4291 (tpt170) REVERT: C 292 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8830 (mp) REVERT: D 85 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7370 (mmp80) REVERT: D 285 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: E 118 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8690 (mp) REVERT: G 425 MET cc_start: -0.2902 (tmt) cc_final: -0.5756 (pp-130) REVERT: M 35 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: N 294 MET cc_start: 0.8446 (mmt) cc_final: 0.7728 (mmt) REVERT: N 354 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: N 373 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7265 (mtt180) REVERT: N 392 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8419 (tttm) REVERT: O 705 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7875 (mtt) REVERT: O 732 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6995 (mtp) REVERT: P 50 THR cc_start: 0.8794 (t) cc_final: 0.8298 (m) REVERT: P 104 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7878 (mt0) outliers start: 126 outliers final: 78 residues processed: 394 average time/residue: 0.6957 time to fit residues: 316.6338 Evaluate side-chains 381 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 291 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 283 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 365 GLN 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 B residue 167 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 290 MET 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 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 532 ARG 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 239 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 322 LYS 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 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 528 THR Chi-restraints excluded: chain G residue 538 LYS 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 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 578 MET Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 35 GLN 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 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 354 GLU Chi-restraints excluded: chain N residue 373 ARG 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 68 ASP Chi-restraints excluded: chain P residue 86 LYS 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: 0.2980 chunk 195 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 309 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 277 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 315 HIS G 537 GLN H 32 HIS H 58 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 575 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 = 0.4177 r_free = 0.4177 target = 0.182728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151910 restraints weight = 34135.380| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.74 r_work: 0.3558 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28518 Z= 0.132 Angle : 0.609 14.105 39036 Z= 0.319 Chirality : 0.043 0.267 4483 Planarity : 0.005 0.098 4765 Dihedral : 13.379 169.797 4842 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 2.75 % Allowed : 19.27 % Favored : 77.98 % 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: 0.43 (0.15), residues: 3251 helix: 1.58 (0.16), residues: 1155 sheet: 0.71 (0.18), residues: 745 loop : -1.13 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 334 TYR 0.018 0.001 TYR C 431 PHE 0.020 0.001 PHE I 93 TRP 0.025 0.002 TRP C 282 HIS 0.010 0.001 HIS M 131 Details of bonding type rmsd covalent geometry : bond 0.00273 (28497) covalent geometry : angle 0.60579 (39027) hydrogen bonds : bond 0.06297 ( 1071) hydrogen bonds : angle 4.16293 ( 2986) metal coordination : bond 0.01129 ( 20) metal coordination : angle 3.87699 ( 9) Misc. bond : bond 0.00036 ( 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 385 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 305 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8974 (mtm) cc_final: 0.8344 (mtm) REVERT: C 168 ARG cc_start: 0.6097 (ptm160) cc_final: 0.4286 (tpt170) REVERT: C 292 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (mp) REVERT: D 85 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7058 (mmp80) REVERT: E 118 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8611 (mp) REVERT: F 372 MET cc_start: 0.7688 (mmt) cc_final: 0.7453 (mmt) REVERT: G 425 MET cc_start: -0.3089 (tmt) cc_final: -0.5674 (pp-130) REVERT: H 98 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8153 (ttm110) REVERT: N 294 MET cc_start: 0.8378 (mmt) cc_final: 0.7488 (mmt) REVERT: O 705 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7688 (mtt) REVERT: P 50 THR cc_start: 0.8754 (t) cc_final: 0.8380 (m) REVERT: P 86 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7825 (mtmm) REVERT: P 104 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7609 (mt0) outliers start: 80 outliers final: 55 residues processed: 358 average time/residue: 0.6780 time to fit residues: 280.4299 Evaluate side-chains 349 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 288 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 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 100 THR 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 157 VAL 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 488 ARG 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 315 HIS 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 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 528 THR 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 K residue 578 MET Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 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 O residue 705 MET Chi-restraints excluded: chain P residue 86 LYS 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: 0.0070 chunk 181 optimal weight: 0.2980 chunk 251 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 315 HIS F 349 GLN G 537 GLN H 58 HIS ** J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 575 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 = 0.4190 r_free = 0.4190 target = 0.184027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154036 restraints weight = 34064.789| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.70 r_work: 0.3589 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28518 Z= 0.125 Angle : 0.595 13.643 39036 Z= 0.310 Chirality : 0.043 0.256 4483 Planarity : 0.005 0.080 4765 Dihedral : 13.327 173.183 4842 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 2.51 % Allowed : 19.72 % Favored : 77.77 % 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: 1.74 (0.16), residues: 1155 sheet: 0.79 (0.18), residues: 757 loop : -1.12 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 334 TYR 0.025 0.001 TYR I 195 PHE 0.028 0.001 PHE L 39 TRP 0.020 0.001 TRP C 282 HIS 0.027 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00258 (28497) covalent geometry : angle 0.59237 (39027) hydrogen bonds : bond 0.05780 ( 1071) hydrogen bonds : angle 4.03537 ( 2986) metal coordination : bond 0.01223 ( 20) metal coordination : angle 3.59592 ( 9) Misc. bond : bond 0.00010 ( 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 367 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9015 (mtm) cc_final: 0.8374 (mtm) REVERT: C 168 ARG cc_start: 0.6015 (ptm160) cc_final: 0.4277 (tpt170) REVERT: C 292 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8800 (mp) REVERT: D 85 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7077 (mmp80) REVERT: D 123 MET cc_start: 0.8108 (mtp) cc_final: 0.7557 (mtp) REVERT: E 118 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8580 (mp) REVERT: F 372 MET cc_start: 0.7598 (mmt) cc_final: 0.7351 (mmt) REVERT: G 425 MET cc_start: -0.3162 (tmt) cc_final: -0.5679 (pp-130) REVERT: H 98 ARG cc_start: 0.8404 (ttm110) cc_final: 0.8142 (ttm110) REVERT: J 68 ASP cc_start: 0.7020 (p0) cc_final: 0.6798 (p0) REVERT: K 500 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4857 (pp) REVERT: N 294 MET cc_start: 0.8354 (mmt) cc_final: 0.7546 (mmt) REVERT: P 50 THR cc_start: 0.8735 (t) cc_final: 0.8389 (m) REVERT: P 86 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7896 (mtmm) REVERT: P 104 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7539 (mt0) outliers start: 73 outliers final: 50 residues processed: 345 average time/residue: 0.6974 time to fit residues: 278.2674 Evaluate side-chains 342 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 347 LEU 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 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 488 ARG 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 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 310 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 528 THR 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 K residue 500 LEU Chi-restraints excluded: chain K residue 578 MET Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 142 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 P residue 49 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 104 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 321 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 chunk 282 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 348 ASN F 349 GLN G 537 GLN H 58 HIS I 164 GLN ** J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 486 HIS ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN P 58 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151332 restraints weight = 33957.960| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.87 r_work: 0.3547 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28518 Z= 0.142 Angle : 0.617 13.169 39036 Z= 0.321 Chirality : 0.044 0.250 4483 Planarity : 0.005 0.104 4765 Dihedral : 13.335 172.536 4840 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.34 % Allowed : 19.82 % Favored : 77.84 % 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: 0.52 (0.15), residues: 3251 helix: 1.70 (0.16), residues: 1153 sheet: 0.75 (0.18), residues: 754 loop : -1.12 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 334 TYR 0.016 0.001 TYR C 596 PHE 0.033 0.002 PHE L 30 TRP 0.019 0.002 TRP C 282 HIS 0.011 0.001 HIS J 58 Details of bonding type rmsd covalent geometry : bond 0.00314 (28497) covalent geometry : angle 0.61371 (39027) hydrogen bonds : bond 0.06327 ( 1071) hydrogen bonds : angle 4.06704 ( 2986) metal coordination : bond 0.01327 ( 20) metal coordination : angle 4.06753 ( 9) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10518.84 seconds wall clock time: 179 minutes 22.72 seconds (10762.72 seconds total)