Starting phenix.real_space_refine on Sat Jul 4 16:19:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0x_61061/07_2026/9j0x_61061.cif" } resolution = 3.0 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= -0.003 sd= 0.065 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 100 5.16 5 C 14274 2.51 5 N 3686 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22042 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5425 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 19, 'TRANS': 649} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5594 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 19, 'TRANS': 668} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 5425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5425 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 19, 'TRANS': 649} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5594 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 19, 'TRANS': 668} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 5.48, per 1000 atoms: 0.25 Number of scatterers: 22042 At special positions: 0 Unit cell: (119.168, 117.04, 183.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 100 16.00 O 3978 8.00 N 3686 7.00 C 14274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5096 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 16 sheets defined 56.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.756A pdb=" N MET A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 108 through 115 removed outlier: 3.722A pdb=" N ILE A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.900A pdb=" N PHE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.620A pdb=" N ASP A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.674A pdb=" N LEU A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 175 " --> pdb=" O TRP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.710A pdb=" N VAL A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.551A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 282 through 312 removed outlier: 3.763A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 removed outlier: 3.510A pdb=" N ARG A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 Processing helix chain 'A' and resid 355 through 361 removed outlier: 6.218A pdb=" N THR A 358 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 359 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 360 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.878A pdb=" N LYS A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.970A pdb=" N ILE A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.851A pdb=" N THR A 498 " --> pdb=" O HIS A 494 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 removed outlier: 3.909A pdb=" N ILE A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.530A pdb=" N LEU A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 587 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.582A pdb=" N LYS A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.616A pdb=" N VAL A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 removed outlier: 4.297A pdb=" N MET A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.958A pdb=" N LEU A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 715 removed outlier: 4.220A pdb=" N GLU A 714 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 715 " --> pdb=" O LEU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 4.144A pdb=" N ASP B 49 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 50' Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.832A pdb=" N MET B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.558A pdb=" N PHE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 115 removed outlier: 3.776A pdb=" N ASP B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.600A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.711A pdb=" N VAL B 167 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR B 169 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 170 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.600A pdb=" N ILE B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.620A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.690A pdb=" N ILE B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.659A pdb=" N THR B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 312 removed outlier: 3.562A pdb=" N PHE B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 removed outlier: 4.006A pdb=" N LYS B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 351 removed outlier: 3.661A pdb=" N SER B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 391 through 401 removed outlier: 4.097A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 removed outlier: 5.227A pdb=" N LEU B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 505 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 579 through 583 removed outlier: 4.074A pdb=" N LEU B 583 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.761A pdb=" N ALA B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 Processing helix chain 'B' and resid 617 through 620 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.511A pdb=" N VAL B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.540A pdb=" N ALA B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 709 through 718 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.589A pdb=" N MET C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 131 through 143 removed outlier: 4.537A pdb=" N PHE C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.759A pdb=" N ASP C 147 " --> pdb=" O HIS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.678A pdb=" N LEU C 171 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP C 172 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 4.110A pdb=" N VAL C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 225 removed outlier: 3.612A pdb=" N TYR C 210 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.912A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.546A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 5.273A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 312 removed outlier: 3.692A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.596A pdb=" N ARG C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 333 Processing helix chain 'C' and resid 338 through 353 Processing helix chain 'C' and resid 354 through 357 removed outlier: 4.013A pdb=" N ASP C 357 " --> pdb=" O HIS C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 357' Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.645A pdb=" N GLN C 362 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.819A pdb=" N LYS C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 518 through 541 removed outlier: 3.669A pdb=" N ILE C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.674A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 587 removed outlier: 3.522A pdb=" N GLY C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 609 through 617 removed outlier: 3.571A pdb=" N ILE C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 638 removed outlier: 3.523A pdb=" N PHE C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 648 Processing helix chain 'C' and resid 663 through 672 removed outlier: 3.787A pdb=" N GLU C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 682 removed outlier: 3.659A pdb=" N ALA C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 682 " --> pdb=" O LYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.850A pdb=" N GLU C 700 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 712 removed outlier: 3.734A pdb=" N ILE C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 718 removed outlier: 3.722A pdb=" N ASN C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 89 removed outlier: 3.640A pdb=" N TYR D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.514A pdb=" N PHE D 89 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 115 removed outlier: 3.676A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.632A pdb=" N ILE D 173 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 195 through 209 removed outlier: 3.742A pdb=" N LEU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 227 through 234 removed outlier: 3.645A pdb=" N GLU D 231 " --> pdb=" O PRO D 228 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.538A pdb=" N ILE D 252 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 282 through 312 removed outlier: 3.544A pdb=" N SER D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 338 through 345 removed outlier: 3.503A pdb=" N THR D 344 " --> pdb=" O ARG D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 377 Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 483 through 492 removed outlier: 5.299A pdb=" N LEU D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 502 Processing helix chain 'D' and resid 504 through 508 removed outlier: 3.704A pdb=" N GLU D 508 " --> pdb=" O GLU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.791A pdb=" N GLN D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.781A pdb=" N ALA D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS D 573 " --> pdb=" O HIS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 584 removed outlier: 3.534A pdb=" N PHE D 582 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 583 " --> pdb=" O THR D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 609 through 616 Processing helix chain 'D' and resid 617 through 619 No H-bonds generated for 'chain 'D' and resid 617 through 619' Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.736A pdb=" N ALA D 637 " --> pdb=" O CYS D 633 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 639 " --> pdb=" O THR D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 650 removed outlier: 3.752A pdb=" N SER D 650 " --> pdb=" O ARG D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 676 through 683 removed outlier: 3.710A pdb=" N ALA D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 713 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.819A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.753A pdb=" N VAL A 469 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 435 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A 444 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.980A pdb=" N THR A 452 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.578A pdb=" N PHE B 407 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 452 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 446 removed outlier: 3.837A pdb=" N GLU B 443 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 435 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 433 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 430 " --> pdb=" O CYS B 472 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.721A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB3, first strand: chain 'C' and resid 442 through 448 removed outlier: 7.275A pdb=" N ALA C 433 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU C 447 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU C 431 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.544A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 403 through 407 removed outlier: 3.679A pdb=" N PHE D 407 " --> pdb=" O CYS D 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 412 through 414 removed outlier: 6.894A pdb=" N VAL D 469 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU D 430 " --> pdb=" O CYS D 472 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR D 446 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL D 435 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER D 444 " --> pdb=" O VAL D 435 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4101 1.33 - 1.45: 5790 1.45 - 1.57: 12505 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 22552 Sorted by residual: bond pdb=" C ASN A 501 " pdb=" N ASN A 502 " ideal model delta sigma weight residual 1.334 1.537 -0.203 1.43e-02 4.89e+03 2.01e+02 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.524 1.405 0.118 1.44e-02 4.82e+03 6.75e+01 bond pdb=" CA ALA B 572 " pdb=" C ALA B 572 " ideal model delta sigma weight residual 1.523 1.423 0.100 1.30e-02 5.92e+03 5.90e+01 bond pdb=" N ALA B 572 " pdb=" CA ALA B 572 " ideal model delta sigma weight residual 1.459 1.388 0.072 1.21e-02 6.83e+03 3.50e+01 bond pdb=" N CYS B 573 " pdb=" CA CYS B 573 " ideal model delta sigma weight residual 1.457 1.384 0.072 1.25e-02 6.40e+03 3.36e+01 ... (remaining 22547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 30347 5.53 - 11.05: 123 11.05 - 16.58: 9 16.58 - 22.11: 2 22.11 - 27.63: 3 Bond angle restraints: 30484 Sorted by residual: angle pdb=" N VAL B 521 " pdb=" CA VAL B 521 " pdb=" C VAL B 521 " ideal model delta sigma weight residual 108.36 85.74 22.62 1.43e+00 4.89e-01 2.50e+02 angle pdb=" N GLU B 577 " pdb=" CA GLU B 577 " pdb=" C GLU B 577 " ideal model delta sigma weight residual 110.80 138.43 -27.63 2.13e+00 2.20e-01 1.68e+02 angle pdb=" C ASN A 501 " pdb=" N ASN A 502 " pdb=" CA ASN A 502 " ideal model delta sigma weight residual 120.58 139.45 -18.87 1.71e+00 3.42e-01 1.22e+02 angle pdb=" N LYS A 514 " pdb=" CA LYS A 514 " pdb=" C LYS A 514 " ideal model delta sigma weight residual 111.07 99.41 11.66 1.07e+00 8.73e-01 1.19e+02 angle pdb=" N LEU A 516 " pdb=" CA LEU A 516 " pdb=" C LEU A 516 " ideal model delta sigma weight residual 110.80 88.22 22.58 2.13e+00 2.20e-01 1.12e+02 ... (remaining 30479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 12035 17.68 - 35.37: 1112 35.37 - 53.05: 197 53.05 - 70.73: 23 70.73 - 88.42: 11 Dihedral angle restraints: 13378 sinusoidal: 5440 harmonic: 7938 Sorted by residual: dihedral pdb=" C ASP B 578 " pdb=" N ASP B 578 " pdb=" CA ASP B 578 " pdb=" CB ASP B 578 " ideal model delta harmonic sigma weight residual -122.60 -142.04 19.44 0 2.50e+00 1.60e-01 6.05e+01 dihedral pdb=" CA ALA C 621 " pdb=" C ALA C 621 " pdb=" N SER C 622 " pdb=" CA SER C 622 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" N LYS A 514 " pdb=" C LYS A 514 " pdb=" CA LYS A 514 " pdb=" CB LYS A 514 " ideal model delta harmonic sigma weight residual 122.80 109.38 13.42 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 13375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3278 0.142 - 0.284: 74 0.284 - 0.426: 8 0.426 - 0.568: 2 0.568 - 0.710: 2 Chirality restraints: 3364 Sorted by residual: chirality pdb=" CA GLU B 577 " pdb=" N GLU B 577 " pdb=" C GLU B 577 " pdb=" CB GLU B 577 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA ASP B 578 " pdb=" N ASP B 578 " pdb=" C ASP B 578 " pdb=" CB ASP B 578 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA LEU A 516 " pdb=" N LEU A 516 " pdb=" C LEU A 516 " pdb=" CB LEU A 516 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 3361 not shown) Planarity restraints: 3854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 606 " -0.021 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C LYS B 606 " 0.078 2.00e-02 2.50e+03 pdb=" O LYS B 606 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA B 607 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 578 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ASP B 578 " 0.076 2.00e-02 2.50e+03 pdb=" O ASP B 578 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE B 579 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 504 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C MET A 504 " 0.062 2.00e-02 2.50e+03 pdb=" O MET A 504 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU A 505 " -0.021 2.00e-02 2.50e+03 ... (remaining 3851 not shown) Histogram of nonbonded interaction distances: 1.22 - 2.00: 3 2.00 - 2.79: 5556 2.79 - 3.57: 34318 3.57 - 4.36: 64472 4.36 - 5.14: 111226 Nonbonded interactions: 215575 Sorted by model distance: nonbonded pdb=" CD1 LEU C 644 " pdb=" CE MET C 676 " model vdw 1.217 3.880 nonbonded pdb=" CG1 ILE D 579 " pdb=" CE2 PHE D 582 " model vdw 1.908 3.740 nonbonded pdb=" O GLU B 508 " pdb=" CD2 LEU B 516 " model vdw 1.938 3.460 nonbonded pdb=" OH TYR A 545 " pdb=" OE2 GLU B 517 " model vdw 2.006 3.040 nonbonded pdb=" CG1 ILE D 579 " pdb=" CD2 PHE D 582 " model vdw 2.062 3.740 ... (remaining 215570 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 'A' and resid 52 through 720) selection = (chain 'B' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 720)) selection = (chain 'C' and resid 52 through 720) selection = (chain 'D' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 720)) } 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: 4.000 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 21.120 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 22552 Z= 0.289 Angle : 1.027 27.634 30484 Z= 0.590 Chirality : 0.061 0.710 3364 Planarity : 0.007 0.075 3854 Dihedral : 13.894 88.418 8282 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.09 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: -4.85 (0.12), residues: 2706 helix: -3.48 (0.08), residues: 1499 sheet: -2.32 (0.46), residues: 112 loop : -2.68 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 45 TYR 0.029 0.002 TYR B 562 PHE 0.020 0.002 PHE A 623 TRP 0.011 0.001 TRP A 235 HIS 0.008 0.001 HIS C 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.29 (22552) covalent geometry : angle 1.02711 / 0.59 (30484) hydrogen bonds : bond 0.17502 / 11.73 ( 898) hydrogen bonds : angle 7.09324 / 4.97 ( 2535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7261 (tmt170) cc_final: 0.5792 (ptt180) REVERT: A 320 ARG cc_start: 0.7457 (ttm110) cc_final: 0.7170 (ttm110) REVERT: A 337 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7557 (tpm170) REVERT: A 340 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7661 (mtp85) REVERT: A 470 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7353 (mtp-110) REVERT: A 483 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8189 (tp-100) REVERT: A 519 ASP cc_start: 0.8819 (m-30) cc_final: 0.8516 (t0) REVERT: A 613 ILE cc_start: 0.8583 (mt) cc_final: 0.8380 (mp) REVERT: B 37 TRP cc_start: 0.6340 (m100) cc_final: 0.6049 (m100) REVERT: B 63 ARG cc_start: 0.7085 (tmm-80) cc_final: 0.6393 (tmm160) REVERT: B 121 ARG cc_start: 0.7366 (tpm170) cc_final: 0.6982 (tpp-160) REVERT: B 137 PHE cc_start: 0.7234 (m-80) cc_final: 0.6892 (m-10) REVERT: B 301 TYR cc_start: 0.7314 (t80) cc_final: 0.7095 (m-80) REVERT: B 330 MET cc_start: 0.8482 (mtm) cc_final: 0.8200 (mtm) REVERT: B 638 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8942 (mmpt) REVERT: B 666 HIS cc_start: 0.7067 (t70) cc_final: 0.6163 (t-170) REVERT: C 317 GLU cc_start: 0.7534 (pm20) cc_final: 0.7330 (mp0) REVERT: C 351 TYR cc_start: 0.8696 (t80) cc_final: 0.8448 (t80) REVERT: C 403 HIS cc_start: 0.7720 (m-70) cc_final: 0.7363 (m-70) REVERT: C 540 PHE cc_start: 0.8693 (t80) cc_final: 0.8446 (t80) REVERT: C 648 LEU cc_start: 0.8248 (mm) cc_final: 0.7989 (mp) REVERT: C 661 HIS cc_start: 0.8334 (m-70) cc_final: 0.7517 (m170) REVERT: D 432 GLU cc_start: 0.7178 (tt0) cc_final: 0.6535 (tt0) REVERT: D 645 LYS cc_start: 0.9083 (tmmt) cc_final: 0.8752 (mtmm) REVERT: D 661 HIS cc_start: 0.7800 (m90) cc_final: 0.7475 (m170) REVERT: D 666 HIS cc_start: 0.7148 (m-70) cc_final: 0.6624 (m-70) REVERT: D 671 GLU cc_start: 0.8475 (tp30) cc_final: 0.8100 (tp30) REVERT: D 673 LEU cc_start: 0.7881 (mt) cc_final: 0.7503 (mt) REVERT: D 702 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7834 (mtt-85) outliers start: 0 outliers final: 1 residues processed: 384 average time/residue: 0.6434 time to fit residues: 281.2902 Evaluate side-chains 232 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 278 HIS ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN A 416 GLN A 546 GLN A 569 HIS A 624 ASN B 186 GLN B 346 HIS B 350 GLN B 374 GLN B 451 HIS ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 695 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 278 HIS C 569 HIS C 624 ASN C 666 HIS C 695 ASN D 59 HIS D 186 GLN D 230 ASN D 305 ASN D 483 GLN D 487 ASN D 510 ASN ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D 718 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096610 restraints weight = 32067.615| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.20 r_work: 0.3148 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22552 Z= 0.154 Angle : 0.668 15.010 30484 Z= 0.346 Chirality : 0.043 0.211 3364 Planarity : 0.005 0.051 3854 Dihedral : 6.167 85.695 2994 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.61 % Rotamer: Outliers : 2.67 % Allowed : 14.71 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.13 (0.15), residues: 2706 helix: -1.98 (0.12), residues: 1505 sheet: -2.28 (0.43), residues: 127 loop : -1.97 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 552 TYR 0.021 0.001 TYR C 492 PHE 0.019 0.001 PHE C 264 TRP 0.017 0.001 TRP C 255 HIS 0.008 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (22552) covalent geometry : angle 0.66772 / 0.35 (30484) hydrogen bonds : bond 0.03889 / 2.47 ( 898) hydrogen bonds : angle 4.60094 / 3.20 ( 2535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7438 (tmt170) cc_final: 0.5758 (ptt180) REVERT: A 320 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7477 (ttm110) REVERT: A 326 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 337 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.7963 (tpp-160) REVERT: A 340 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.8013 (mtp85) REVERT: A 470 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7727 (mtp-110) REVERT: A 483 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8520 (tp-100) REVERT: A 519 ASP cc_start: 0.8826 (m-30) cc_final: 0.8620 (m-30) REVERT: B 37 TRP cc_start: 0.6233 (m100) cc_final: 0.5966 (m100) REVERT: B 63 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.6543 (tmm160) REVERT: B 121 ARG cc_start: 0.7772 (tpm170) cc_final: 0.7234 (tpp-160) REVERT: B 137 PHE cc_start: 0.7773 (m-80) cc_final: 0.7245 (m-10) REVERT: B 301 TYR cc_start: 0.8107 (t80) cc_final: 0.7559 (m-80) REVERT: B 317 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: B 493 PHE cc_start: 0.8540 (p90) cc_final: 0.8298 (p90) REVERT: B 546 GLN cc_start: 0.9242 (tp-100) cc_final: 0.8583 (tp-100) REVERT: B 666 HIS cc_start: 0.7232 (t70) cc_final: 0.6135 (t-170) REVERT: B 698 LEU cc_start: 0.9251 (tt) cc_final: 0.8923 (mp) REVERT: C 317 GLU cc_start: 0.8036 (pm20) cc_final: 0.7829 (mp0) REVERT: C 479 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7642 (ttp80) REVERT: C 504 MET cc_start: 0.7556 (tpp) cc_final: 0.7269 (mmt) REVERT: C 615 LEU cc_start: 0.9086 (mt) cc_final: 0.8884 (mp) REVERT: C 618 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8860 (mmpt) REVERT: D 51 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5615 (t70) REVERT: D 355 TYR cc_start: 0.6121 (t80) cc_final: 0.5798 (t80) REVERT: D 369 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7876 (mtm180) REVERT: D 432 GLU cc_start: 0.8195 (tt0) cc_final: 0.7647 (tt0) REVERT: D 661 HIS cc_start: 0.7977 (m90) cc_final: 0.7610 (m170) REVERT: D 666 HIS cc_start: 0.7170 (m-70) cc_final: 0.6441 (m-70) REVERT: D 671 GLU cc_start: 0.8783 (tp30) cc_final: 0.8234 (tp30) REVERT: D 673 LEU cc_start: 0.7939 (mt) cc_final: 0.7443 (mt) outliers start: 64 outliers final: 14 residues processed: 307 average time/residue: 0.5358 time to fit residues: 190.0776 Evaluate side-chains 234 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 674 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN B 354 HIS ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 HIS D 510 ASN ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091854 restraints weight = 32358.548| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.15 r_work: 0.3055 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 22552 Z= 0.286 Angle : 0.730 14.178 30484 Z= 0.378 Chirality : 0.047 0.168 3364 Planarity : 0.005 0.049 3854 Dihedral : 5.923 26.280 2992 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.31 % Favored : 90.61 % Rotamer: Outliers : 3.58 % Allowed : 16.29 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.15), residues: 2706 helix: -1.47 (0.12), residues: 1542 sheet: -1.91 (0.47), residues: 114 loop : -1.80 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 662 TYR 0.026 0.002 TYR A 258 PHE 0.020 0.002 PHE A 287 TRP 0.020 0.002 TRP C 255 HIS 0.007 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (22552) covalent geometry : angle 0.72969 / 0.38 (30484) hydrogen bonds : bond 0.04367 / 2.74 ( 898) hydrogen bonds : angle 4.50709 / 3.14 ( 2535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 230 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8965 (mmp) cc_final: 0.8737 (mtp) REVERT: A 96 ARG cc_start: 0.7597 (tmt170) cc_final: 0.5741 (ptt180) REVERT: A 206 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 320 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7497 (ttm110) REVERT: A 337 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.7919 (tpp-160) REVERT: A 340 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7892 (mtm-85) REVERT: A 470 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7704 (mtp-110) REVERT: A 483 GLN cc_start: 0.8854 (tp40) cc_final: 0.8598 (tp40) REVERT: A 623 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 37 TRP cc_start: 0.6177 (m100) cc_final: 0.5926 (m100) REVERT: B 63 ARG cc_start: 0.7605 (tmm-80) cc_final: 0.6545 (tmm160) REVERT: B 121 ARG cc_start: 0.7992 (tpm170) cc_final: 0.7199 (tpp-160) REVERT: B 137 PHE cc_start: 0.7767 (m-80) cc_final: 0.7291 (m-10) REVERT: B 204 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 301 TYR cc_start: 0.8246 (t80) cc_final: 0.7626 (m-80) REVERT: B 317 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: B 546 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8489 (tp-100) REVERT: B 652 MET cc_start: 0.8317 (mmm) cc_final: 0.7887 (tpt) REVERT: B 665 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 666 HIS cc_start: 0.7021 (t70) cc_final: 0.5980 (t-170) REVERT: C 317 GLU cc_start: 0.8159 (pm20) cc_final: 0.7913 (mp0) REVERT: C 405 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7620 (mt-10) REVERT: C 479 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7055 (mtm-85) REVERT: C 504 MET cc_start: 0.7578 (tpp) cc_final: 0.7250 (mmt) REVERT: C 530 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: C 552 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8110 (mpt90) REVERT: C 615 LEU cc_start: 0.9069 (mt) cc_final: 0.8854 (mp) REVERT: C 618 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8922 (mmpt) REVERT: C 661 HIS cc_start: 0.8005 (m-70) cc_final: 0.6951 (m90) REVERT: C 676 MET cc_start: 0.8595 (mmt) cc_final: 0.8322 (mmt) REVERT: D 51 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5965 (t70) REVERT: D 70 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6692 (tmm) REVERT: D 327 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8027 (mp) REVERT: D 369 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7818 (mtm180) REVERT: D 432 GLU cc_start: 0.8217 (tt0) cc_final: 0.7696 (tt0) REVERT: D 493 PHE cc_start: 0.8157 (p90) cc_final: 0.7607 (p90) REVERT: D 666 HIS cc_start: 0.7268 (m-70) cc_final: 0.6505 (m-70) REVERT: D 671 GLU cc_start: 0.8813 (tp30) cc_final: 0.8274 (tp30) REVERT: D 673 LEU cc_start: 0.8013 (mt) cc_final: 0.7583 (mt) REVERT: D 702 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7833 (mtt-85) outliers start: 86 outliers final: 32 residues processed: 291 average time/residue: 0.5786 time to fit residues: 194.7009 Evaluate side-chains 246 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 674 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN B 527 GLN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094965 restraints weight = 32237.524| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.27 r_work: 0.3105 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22552 Z= 0.151 Angle : 0.644 16.545 30484 Z= 0.329 Chirality : 0.043 0.168 3364 Planarity : 0.004 0.050 3854 Dihedral : 5.593 24.964 2992 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.46 % Favored : 91.50 % Rotamer: Outliers : 3.46 % Allowed : 17.62 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.16), residues: 2706 helix: -1.07 (0.13), residues: 1529 sheet: -1.84 (0.45), residues: 130 loop : -1.68 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 193 TYR 0.014 0.001 TYR B 562 PHE 0.045 0.001 PHE C 540 TRP 0.013 0.001 TRP C 255 HIS 0.008 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22552) covalent geometry : angle 0.64382 / 0.33 (30484) hydrogen bonds : bond 0.03557 / 2.22 ( 898) hydrogen bonds : angle 4.14913 / 2.89 ( 2535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7623 (tmt170) cc_final: 0.5749 (ptt180) REVERT: A 193 ARG cc_start: 0.7153 (mtm180) cc_final: 0.6909 (mtm-85) REVERT: A 206 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 320 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7487 (ttm110) REVERT: A 326 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 337 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7948 (tpp-160) REVERT: A 430 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8118 (tm) REVERT: A 470 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7688 (mtp-110) REVERT: A 483 GLN cc_start: 0.8906 (tp40) cc_final: 0.8576 (tp40) REVERT: A 623 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 666 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5504 (m170) REVERT: B 37 TRP cc_start: 0.6163 (m100) cc_final: 0.5870 (m100) REVERT: B 63 ARG cc_start: 0.7590 (tmm-80) cc_final: 0.6613 (tmm160) REVERT: B 121 ARG cc_start: 0.7673 (tpm170) cc_final: 0.7103 (tpp-160) REVERT: B 137 PHE cc_start: 0.7712 (m-80) cc_final: 0.7237 (m-10) REVERT: B 204 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8000 (mm) REVERT: B 301 TYR cc_start: 0.8158 (t80) cc_final: 0.7634 (m-80) REVERT: B 317 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: B 493 PHE cc_start: 0.8655 (p90) cc_final: 0.8414 (p90) REVERT: B 546 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8492 (tp-100) REVERT: B 642 ASP cc_start: 0.8645 (p0) cc_final: 0.8341 (p0) REVERT: B 665 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 666 HIS cc_start: 0.7363 (t70) cc_final: 0.6224 (t-170) REVERT: B 698 LEU cc_start: 0.9113 (tt) cc_final: 0.8874 (mp) REVERT: C 317 GLU cc_start: 0.8168 (pm20) cc_final: 0.7908 (mp0) REVERT: C 405 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7765 (mt-10) REVERT: C 479 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: C 504 MET cc_start: 0.7604 (tpp) cc_final: 0.7266 (mmt) REVERT: C 574 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8477 (mmm-85) REVERT: C 615 LEU cc_start: 0.9025 (mt) cc_final: 0.8798 (mp) REVERT: C 618 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8872 (mmpt) REVERT: C 661 HIS cc_start: 0.7974 (m-70) cc_final: 0.6919 (m90) REVERT: D 51 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.6062 (t70) REVERT: D 70 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6641 (tmt) REVERT: D 369 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7902 (mtm180) REVERT: D 432 GLU cc_start: 0.8245 (tt0) cc_final: 0.7726 (tt0) REVERT: D 436 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7387 (t) REVERT: D 481 ASP cc_start: 0.7842 (p0) cc_final: 0.7469 (t0) REVERT: D 642 ASP cc_start: 0.8712 (m-30) cc_final: 0.8341 (m-30) REVERT: D 645 LYS cc_start: 0.9129 (tptp) cc_final: 0.8685 (mtmm) REVERT: D 666 HIS cc_start: 0.7128 (m-70) cc_final: 0.6383 (m-70) REVERT: D 671 GLU cc_start: 0.8787 (tp30) cc_final: 0.8253 (tp30) REVERT: D 673 LEU cc_start: 0.7980 (mt) cc_final: 0.7515 (mt) REVERT: D 702 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7646 (mtt-85) outliers start: 83 outliers final: 26 residues processed: 284 average time/residue: 0.5605 time to fit residues: 185.2886 Evaluate side-chains 251 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 676 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 167 optimal weight: 0.0270 chunk 225 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096048 restraints weight = 31836.467| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.19 r_work: 0.3127 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22552 Z= 0.135 Angle : 0.633 17.344 30484 Z= 0.320 Chirality : 0.043 0.173 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.348 25.506 2992 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.50 % Favored : 91.46 % Rotamer: Outliers : 3.17 % Allowed : 18.29 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2706 helix: -0.77 (0.13), residues: 1509 sheet: -1.73 (0.45), residues: 130 loop : -1.53 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.017 0.001 TYR D 355 PHE 0.017 0.001 PHE D 544 TRP 0.012 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (22552) covalent geometry : angle 0.63295 / 0.32 (30484) hydrogen bonds : bond 0.03377 / 2.11 ( 898) hydrogen bonds : angle 4.03109 / 2.79 ( 2535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 227 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7639 (tmt170) cc_final: 0.5808 (ptt180) REVERT: A 193 ARG cc_start: 0.7159 (mtm180) cc_final: 0.6919 (mtm-85) REVERT: A 206 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 320 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7479 (ttm110) REVERT: A 337 ARG cc_start: 0.8464 (tpp-160) cc_final: 0.7968 (tpp-160) REVERT: A 408 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8456 (mm) REVERT: A 430 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8132 (tm) REVERT: A 470 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7692 (mtp-110) REVERT: A 483 GLN cc_start: 0.8953 (tp40) cc_final: 0.8640 (tp40) REVERT: A 623 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: B 37 TRP cc_start: 0.6151 (m100) cc_final: 0.5856 (m100) REVERT: B 63 ARG cc_start: 0.7578 (tmm-80) cc_final: 0.6597 (tmm160) REVERT: B 121 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7013 (tpp-160) REVERT: B 137 PHE cc_start: 0.7788 (m-80) cc_final: 0.7169 (m-10) REVERT: B 204 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8005 (mm) REVERT: B 301 TYR cc_start: 0.8124 (t80) cc_final: 0.7599 (m-80) REVERT: B 317 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 360 MET cc_start: 0.9144 (ppp) cc_final: 0.8599 (ppp) REVERT: B 493 PHE cc_start: 0.8646 (p90) cc_final: 0.8388 (p90) REVERT: B 546 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8456 (tp-100) REVERT: B 610 GLU cc_start: 0.7024 (pm20) cc_final: 0.6817 (pm20) REVERT: B 642 ASP cc_start: 0.8644 (p0) cc_final: 0.8411 (p0) REVERT: B 652 MET cc_start: 0.8253 (mmm) cc_final: 0.7846 (tpt) REVERT: B 665 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 666 HIS cc_start: 0.7377 (t70) cc_final: 0.6307 (t-170) REVERT: B 673 LEU cc_start: 0.8001 (mm) cc_final: 0.7574 (mp) REVERT: B 698 LEU cc_start: 0.8988 (tt) cc_final: 0.8773 (mp) REVERT: C 210 TYR cc_start: 0.8396 (m-80) cc_final: 0.8140 (m-80) REVERT: C 351 TYR cc_start: 0.8760 (t80) cc_final: 0.8547 (t80) REVERT: C 405 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 479 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: C 530 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: C 540 PHE cc_start: 0.8307 (t80) cc_final: 0.7857 (t80) REVERT: C 574 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: C 615 LEU cc_start: 0.9003 (mt) cc_final: 0.8735 (mp) REVERT: C 618 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8874 (mmpt) REVERT: C 661 HIS cc_start: 0.8013 (m-70) cc_final: 0.6926 (m90) REVERT: C 676 MET cc_start: 0.8295 (mmt) cc_final: 0.8080 (mmt) REVERT: D 51 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.6060 (t70) REVERT: D 70 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6617 (tmt) REVERT: D 369 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7850 (mtm180) REVERT: D 432 GLU cc_start: 0.8202 (tt0) cc_final: 0.7741 (tt0) REVERT: D 481 ASP cc_start: 0.7737 (p0) cc_final: 0.7490 (t0) REVERT: D 524 ILE cc_start: 0.3166 (OUTLIER) cc_final: 0.2843 (mp) REVERT: D 642 ASP cc_start: 0.8608 (m-30) cc_final: 0.8344 (m-30) REVERT: D 645 LYS cc_start: 0.9089 (tptp) cc_final: 0.8587 (mtmm) REVERT: D 666 HIS cc_start: 0.7110 (m-70) cc_final: 0.6327 (m-70) REVERT: D 671 GLU cc_start: 0.8752 (tp30) cc_final: 0.8151 (tp30) REVERT: D 673 LEU cc_start: 0.7869 (mt) cc_final: 0.7273 (mt) REVERT: D 702 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7635 (mtt-85) outliers start: 76 outliers final: 24 residues processed: 277 average time/residue: 0.5363 time to fit residues: 173.3937 Evaluate side-chains 246 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 62 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.152830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093389 restraints weight = 32348.934| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.21 r_work: 0.3080 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22552 Z= 0.196 Angle : 0.672 18.434 30484 Z= 0.339 Chirality : 0.044 0.167 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.374 25.437 2992 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.91 % Favored : 91.06 % Rotamer: Outliers : 3.92 % Allowed : 17.92 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2706 helix: -0.71 (0.13), residues: 1517 sheet: -1.71 (0.46), residues: 130 loop : -1.44 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 552 TYR 0.022 0.001 TYR A 258 PHE 0.017 0.002 PHE D 544 TRP 0.015 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (22552) covalent geometry : angle 0.67194 / 0.34 (30484) hydrogen bonds : bond 0.03677 / 2.29 ( 898) hydrogen bonds : angle 4.12494 / 2.87 ( 2535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 225 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7633 (tmt170) cc_final: 0.5744 (ptt180) REVERT: A 193 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6976 (mtm-85) REVERT: A 206 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7305 (t80) REVERT: A 320 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7507 (ttm110) REVERT: A 337 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.7918 (tpp-160) REVERT: A 408 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 430 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8058 (tm) REVERT: A 470 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7681 (mtp-110) REVERT: A 483 GLN cc_start: 0.8992 (tp40) cc_final: 0.8658 (tp40) REVERT: A 623 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: B 37 TRP cc_start: 0.6187 (m100) cc_final: 0.5880 (m100) REVERT: B 63 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.6575 (tmm160) REVERT: B 121 ARG cc_start: 0.7643 (tpm170) cc_final: 0.6834 (tpp-160) REVERT: B 137 PHE cc_start: 0.7828 (m-80) cc_final: 0.7206 (m-10) REVERT: B 204 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8015 (mm) REVERT: B 301 TYR cc_start: 0.8157 (t80) cc_final: 0.7571 (m-80) REVERT: B 317 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: B 493 PHE cc_start: 0.8639 (p90) cc_final: 0.8392 (p90) REVERT: B 546 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8354 (tp-100) REVERT: B 550 LEU cc_start: 0.9146 (mt) cc_final: 0.8531 (mt) REVERT: B 642 ASP cc_start: 0.8706 (p0) cc_final: 0.8365 (p0) REVERT: B 652 MET cc_start: 0.8261 (mmm) cc_final: 0.7765 (tpt) REVERT: B 665 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7438 (tt) REVERT: B 666 HIS cc_start: 0.7302 (t70) cc_final: 0.6251 (t-170) REVERT: B 673 LEU cc_start: 0.7961 (mm) cc_final: 0.7568 (mp) REVERT: B 698 LEU cc_start: 0.9007 (tt) cc_final: 0.8797 (mp) REVERT: B 699 ASP cc_start: 0.8282 (p0) cc_final: 0.8020 (p0) REVERT: C 405 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 479 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7271 (mtm-85) REVERT: C 530 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 540 PHE cc_start: 0.8404 (t80) cc_final: 0.7818 (t80) REVERT: C 552 ARG cc_start: 0.8836 (mtt90) cc_final: 0.8539 (mmt-90) REVERT: C 574 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8323 (mmm-85) REVERT: C 615 LEU cc_start: 0.9012 (mt) cc_final: 0.8722 (mp) REVERT: C 618 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8890 (mmpt) REVERT: C 661 HIS cc_start: 0.8004 (m-70) cc_final: 0.6942 (m90) REVERT: D 51 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.6231 (t70) REVERT: D 70 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6781 (tmt) REVERT: D 112 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8148 (tp) REVERT: D 337 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7803 (ptm-80) REVERT: D 369 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7782 (mtm180) REVERT: D 432 GLU cc_start: 0.8228 (tt0) cc_final: 0.7692 (tt0) REVERT: D 460 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7925 (pt) REVERT: D 481 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7386 (t0) REVERT: D 524 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3520 (mp) REVERT: D 544 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: D 545 TYR cc_start: 0.8604 (m-80) cc_final: 0.8365 (m-80) REVERT: D 642 ASP cc_start: 0.8726 (m-30) cc_final: 0.8518 (m-30) REVERT: D 645 LYS cc_start: 0.9107 (tptp) cc_final: 0.8490 (mtmm) REVERT: D 666 HIS cc_start: 0.7086 (m-70) cc_final: 0.6316 (m-70) REVERT: D 671 GLU cc_start: 0.8838 (tp30) cc_final: 0.8225 (tp30) REVERT: D 673 LEU cc_start: 0.7823 (mt) cc_final: 0.7261 (mt) REVERT: D 702 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7975 (mtm-85) outliers start: 94 outliers final: 41 residues processed: 292 average time/residue: 0.5537 time to fit residues: 189.2197 Evaluate side-chains 273 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 252 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096063 restraints weight = 31882.693| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.22 r_work: 0.3121 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22552 Z= 0.136 Angle : 0.650 19.299 30484 Z= 0.325 Chirality : 0.043 0.210 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.219 25.095 2992 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.39 % Favored : 91.57 % Rotamer: Outliers : 3.21 % Allowed : 19.71 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2706 helix: -0.59 (0.13), residues: 1516 sheet: -1.60 (0.46), residues: 130 loop : -1.30 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 552 TYR 0.020 0.001 TYR D 355 PHE 0.019 0.001 PHE D 544 TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (22552) covalent geometry : angle 0.64991 / 0.33 (30484) hydrogen bonds : bond 0.03330 / 2.07 ( 898) hydrogen bonds : angle 3.97437 / 2.76 ( 2535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 232 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7635 (tmt170) cc_final: 0.5787 (ptt180) REVERT: A 193 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6893 (mtm-85) REVERT: A 320 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7512 (ttm110) REVERT: A 337 ARG cc_start: 0.8498 (tpp-160) cc_final: 0.7907 (tpp-160) REVERT: A 470 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7679 (mtp-110) REVERT: A 483 GLN cc_start: 0.8995 (tp40) cc_final: 0.8685 (tp40) REVERT: A 623 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: B 37 TRP cc_start: 0.6187 (m100) cc_final: 0.5890 (m100) REVERT: B 63 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.6571 (tmm160) REVERT: B 121 ARG cc_start: 0.7512 (tpm170) cc_final: 0.6951 (tpp-160) REVERT: B 137 PHE cc_start: 0.7808 (m-80) cc_final: 0.7182 (m-10) REVERT: B 192 THR cc_start: 0.9139 (p) cc_final: 0.8933 (t) REVERT: B 204 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 301 TYR cc_start: 0.8117 (t80) cc_final: 0.7587 (m-80) REVERT: B 317 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: B 360 MET cc_start: 0.9146 (ppp) cc_final: 0.8612 (ppp) REVERT: B 493 PHE cc_start: 0.8682 (p90) cc_final: 0.8419 (p90) REVERT: B 552 ARG cc_start: 0.8283 (mmp80) cc_final: 0.7964 (mmp80) REVERT: B 642 ASP cc_start: 0.8663 (p0) cc_final: 0.8369 (p0) REVERT: B 665 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7467 (tt) REVERT: B 673 LEU cc_start: 0.7942 (mm) cc_final: 0.7556 (mp) REVERT: B 702 ARG cc_start: 0.8652 (ppt90) cc_final: 0.8341 (mtt-85) REVERT: C 323 MET cc_start: 0.8397 (ttp) cc_final: 0.8150 (mtm) REVERT: C 405 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 479 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: C 530 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: C 540 PHE cc_start: 0.8346 (t80) cc_final: 0.7784 (t80) REVERT: C 552 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8383 (mmt-90) REVERT: C 574 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8300 (mmm-85) REVERT: C 615 LEU cc_start: 0.9010 (mt) cc_final: 0.8790 (mp) REVERT: C 661 HIS cc_start: 0.8015 (m-70) cc_final: 0.6961 (m90) REVERT: D 70 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6674 (tmt) REVERT: D 369 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7823 (mtm180) REVERT: D 432 GLU cc_start: 0.8224 (tt0) cc_final: 0.7780 (tt0) REVERT: D 481 ASP cc_start: 0.7744 (p0) cc_final: 0.7411 (t0) REVERT: D 545 TYR cc_start: 0.8673 (m-80) cc_final: 0.8456 (m-80) REVERT: D 666 HIS cc_start: 0.7003 (m-70) cc_final: 0.6203 (m-70) REVERT: D 671 GLU cc_start: 0.8854 (tp30) cc_final: 0.8281 (tp30) REVERT: D 673 LEU cc_start: 0.7774 (mt) cc_final: 0.7234 (mt) REVERT: D 702 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7921 (mtm-85) outliers start: 77 outliers final: 31 residues processed: 287 average time/residue: 0.5710 time to fit residues: 190.9037 Evaluate side-chains 249 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 234 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 591 ASN B 585 GLN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.154713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095698 restraints weight = 31827.309| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.17 r_work: 0.3123 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22552 Z= 0.147 Angle : 0.680 19.456 30484 Z= 0.336 Chirality : 0.043 0.239 3364 Planarity : 0.004 0.058 3854 Dihedral : 5.162 25.231 2992 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.57 % Favored : 91.39 % Rotamer: Outliers : 2.92 % Allowed : 20.42 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2706 helix: -0.52 (0.13), residues: 1523 sheet: -1.54 (0.46), residues: 130 loop : -1.29 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 497 TYR 0.019 0.001 TYR A 258 PHE 0.026 0.001 PHE B 582 TRP 0.012 0.001 TRP C 255 HIS 0.008 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (22552) covalent geometry : angle 0.67994 / 0.34 (30484) hydrogen bonds : bond 0.03377 / 2.10 ( 898) hydrogen bonds : angle 3.97413 / 2.75 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7577 (tmt170) cc_final: 0.5804 (ptt180) REVERT: A 193 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6896 (mtm-85) REVERT: A 320 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7554 (ttm110) REVERT: A 337 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.7934 (tpp-160) REVERT: A 470 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7714 (mtp-110) REVERT: A 483 GLN cc_start: 0.8978 (tp40) cc_final: 0.8599 (tp40) REVERT: A 623 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: B 37 TRP cc_start: 0.6217 (m100) cc_final: 0.5900 (m100) REVERT: B 63 ARG cc_start: 0.7595 (tmm-80) cc_final: 0.6609 (tmm160) REVERT: B 121 ARG cc_start: 0.7559 (tpm170) cc_final: 0.6962 (tpp-160) REVERT: B 137 PHE cc_start: 0.7825 (m-80) cc_final: 0.7209 (m-10) REVERT: B 204 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8044 (mm) REVERT: B 301 TYR cc_start: 0.8122 (t80) cc_final: 0.7624 (m-80) REVERT: B 317 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: B 360 MET cc_start: 0.9154 (ppp) cc_final: 0.8595 (ppp) REVERT: B 493 PHE cc_start: 0.8725 (p90) cc_final: 0.8444 (p90) REVERT: B 552 ARG cc_start: 0.8387 (mmp80) cc_final: 0.8155 (mmp80) REVERT: B 642 ASP cc_start: 0.8632 (p0) cc_final: 0.8334 (p0) REVERT: B 652 MET cc_start: 0.8244 (mmm) cc_final: 0.7913 (tpt) REVERT: B 673 LEU cc_start: 0.8016 (mm) cc_final: 0.7673 (mp) REVERT: B 699 ASP cc_start: 0.8322 (p0) cc_final: 0.8085 (p0) REVERT: C 319 PHE cc_start: 0.8697 (t80) cc_final: 0.8432 (t80) REVERT: C 323 MET cc_start: 0.8402 (ttp) cc_final: 0.8089 (mtm) REVERT: C 405 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 479 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7391 (mtm-85) REVERT: C 530 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: C 540 PHE cc_start: 0.8438 (t80) cc_final: 0.7815 (t80) REVERT: C 552 ARG cc_start: 0.8863 (mtt90) cc_final: 0.8472 (mmt-90) REVERT: C 574 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8303 (mmm-85) REVERT: C 615 LEU cc_start: 0.9032 (mt) cc_final: 0.8785 (mp) REVERT: C 661 HIS cc_start: 0.8034 (m-70) cc_final: 0.6982 (m90) REVERT: D 64 TRP cc_start: 0.8433 (m100) cc_final: 0.7761 (m-10) REVERT: D 70 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6771 (tmt) REVERT: D 126 TYR cc_start: 0.7478 (m-10) cc_final: 0.7255 (m-10) REVERT: D 369 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7884 (mtm180) REVERT: D 432 GLU cc_start: 0.8243 (tt0) cc_final: 0.7827 (tt0) REVERT: D 481 ASP cc_start: 0.7755 (p0) cc_final: 0.7458 (t0) REVERT: D 543 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7726 (p0) REVERT: D 645 LYS cc_start: 0.9113 (tptp) cc_final: 0.8560 (mtmm) REVERT: D 666 HIS cc_start: 0.6991 (m-70) cc_final: 0.6217 (m-70) REVERT: D 671 GLU cc_start: 0.8822 (tp30) cc_final: 0.8252 (tp30) REVERT: D 673 LEU cc_start: 0.7747 (mt) cc_final: 0.7198 (mt) outliers start: 70 outliers final: 41 residues processed: 272 average time/residue: 0.5270 time to fit residues: 167.1924 Evaluate side-chains 258 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 242 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS B 558 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096889 restraints weight = 31743.467| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.26 r_work: 0.3128 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22552 Z= 0.144 Angle : 0.689 19.790 30484 Z= 0.338 Chirality : 0.043 0.195 3364 Planarity : 0.004 0.077 3854 Dihedral : 5.121 25.220 2992 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 2.38 % Allowed : 21.25 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2706 helix: -0.47 (0.13), residues: 1532 sheet: -1.59 (0.45), residues: 135 loop : -1.24 (0.21), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 702 TYR 0.024 0.001 TYR B 120 PHE 0.028 0.001 PHE B 582 TRP 0.011 0.001 TRP C 255 HIS 0.009 0.001 HIS C 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (22552) covalent geometry : angle 0.68871 / 0.34 (30484) hydrogen bonds : bond 0.03343 / 2.08 ( 898) hydrogen bonds : angle 3.97118 / 2.75 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7574 (tmt170) cc_final: 0.5804 (ptt180) REVERT: A 193 ARG cc_start: 0.7156 (mtm180) cc_final: 0.6906 (mtm-85) REVERT: A 320 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7578 (ttm110) REVERT: A 337 ARG cc_start: 0.8525 (tpp-160) cc_final: 0.7927 (tpp-160) REVERT: A 408 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 470 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7727 (mtp-110) REVERT: A 483 GLN cc_start: 0.8957 (tp40) cc_final: 0.8634 (tp40) REVERT: A 623 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 37 TRP cc_start: 0.6138 (m100) cc_final: 0.5857 (m100) REVERT: B 63 ARG cc_start: 0.7610 (tmm-80) cc_final: 0.6630 (tmm160) REVERT: B 121 ARG cc_start: 0.7552 (tpm170) cc_final: 0.7043 (tpp-160) REVERT: B 137 PHE cc_start: 0.7809 (m-80) cc_final: 0.7189 (m-10) REVERT: B 204 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 301 TYR cc_start: 0.8110 (t80) cc_final: 0.7608 (m-80) REVERT: B 317 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: B 360 MET cc_start: 0.9119 (ppp) cc_final: 0.8506 (ppp) REVERT: B 493 PHE cc_start: 0.8742 (p90) cc_final: 0.8457 (p90) REVERT: B 550 LEU cc_start: 0.9027 (mt) cc_final: 0.8702 (mp) REVERT: B 552 ARG cc_start: 0.8405 (mmp80) cc_final: 0.8138 (mmp80) REVERT: B 642 ASP cc_start: 0.8659 (p0) cc_final: 0.8357 (p0) REVERT: B 652 MET cc_start: 0.8277 (mmm) cc_final: 0.7814 (tpt) REVERT: B 673 LEU cc_start: 0.8004 (mm) cc_final: 0.7696 (mp) REVERT: B 702 ARG cc_start: 0.8567 (ppt90) cc_final: 0.8288 (mtt180) REVERT: C 319 PHE cc_start: 0.8687 (t80) cc_final: 0.8403 (t80) REVERT: C 323 MET cc_start: 0.8416 (ttp) cc_final: 0.8106 (mtm) REVERT: C 351 TYR cc_start: 0.8666 (t80) cc_final: 0.8322 (t80) REVERT: C 405 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 479 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: C 530 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: C 540 PHE cc_start: 0.8401 (t80) cc_final: 0.8110 (t80) REVERT: C 552 ARG cc_start: 0.8865 (mtt90) cc_final: 0.8480 (mmt-90) REVERT: C 615 LEU cc_start: 0.9037 (mt) cc_final: 0.8788 (mp) REVERT: C 661 HIS cc_start: 0.8035 (m-70) cc_final: 0.6976 (m90) REVERT: D 64 TRP cc_start: 0.8440 (m100) cc_final: 0.7782 (m-10) REVERT: D 70 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6769 (tmt) REVERT: D 126 TYR cc_start: 0.7516 (m-10) cc_final: 0.7295 (m-10) REVERT: D 369 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7885 (mtm180) REVERT: D 432 GLU cc_start: 0.8283 (tt0) cc_final: 0.7866 (tt0) REVERT: D 481 ASP cc_start: 0.7740 (p0) cc_final: 0.7463 (t0) REVERT: D 493 PHE cc_start: 0.8140 (p90) cc_final: 0.7714 (p90) REVERT: D 494 HIS cc_start: 0.8089 (m170) cc_final: 0.7872 (m-70) REVERT: D 543 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7644 (p0) REVERT: D 645 LYS cc_start: 0.9123 (tptp) cc_final: 0.8557 (mtmm) REVERT: D 666 HIS cc_start: 0.7010 (m-70) cc_final: 0.6228 (m-70) REVERT: D 671 GLU cc_start: 0.8779 (tp30) cc_final: 0.8156 (tp30) REVERT: D 673 LEU cc_start: 0.7727 (mt) cc_final: 0.7061 (mt) REVERT: D 702 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7682 (mtm-85) outliers start: 57 outliers final: 38 residues processed: 261 average time/residue: 0.5546 time to fit residues: 168.4770 Evaluate side-chains 250 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 248 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 231 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.154845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095194 restraints weight = 31885.565| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.12 r_work: 0.3130 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22552 Z= 0.161 Angle : 0.695 19.867 30484 Z= 0.343 Chirality : 0.044 0.181 3364 Planarity : 0.004 0.081 3854 Dihedral : 5.137 25.295 2992 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.28 % Favored : 91.69 % Rotamer: Outliers : 2.50 % Allowed : 21.33 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2706 helix: -0.43 (0.13), residues: 1531 sheet: -1.62 (0.44), residues: 135 loop : -1.22 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 702 TYR 0.017 0.001 TYR A 258 PHE 0.029 0.001 PHE A 540 TRP 0.012 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (22552) covalent geometry : angle 0.69532 / 0.34 (30484) hydrogen bonds : bond 0.03473 / 2.16 ( 898) hydrogen bonds : angle 4.04024 / 2.81 ( 2535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7533 (tmt170) cc_final: 0.5770 (ptt180) REVERT: A 193 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6891 (mtm-85) REVERT: A 320 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7578 (ttm110) REVERT: A 337 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.7890 (tpp-160) REVERT: A 408 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8400 (mm) REVERT: A 470 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7700 (mtp-110) REVERT: A 483 GLN cc_start: 0.8970 (tp40) cc_final: 0.8620 (tp40) REVERT: A 623 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: B 37 TRP cc_start: 0.6165 (m100) cc_final: 0.5891 (m100) REVERT: B 63 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.6606 (tmm160) REVERT: B 121 ARG cc_start: 0.7635 (tpm170) cc_final: 0.7091 (tpp-160) REVERT: B 137 PHE cc_start: 0.7808 (m-80) cc_final: 0.7192 (m-10) REVERT: B 204 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 301 TYR cc_start: 0.8091 (t80) cc_final: 0.7583 (m-80) REVERT: B 317 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: B 360 MET cc_start: 0.9096 (ppp) cc_final: 0.8607 (ppp) REVERT: B 493 PHE cc_start: 0.8728 (p90) cc_final: 0.8470 (p90) REVERT: B 550 LEU cc_start: 0.9015 (mt) cc_final: 0.8691 (mp) REVERT: B 552 ARG cc_start: 0.8385 (mmp80) cc_final: 0.8155 (mmp80) REVERT: B 642 ASP cc_start: 0.8664 (p0) cc_final: 0.8377 (p0) REVERT: B 652 MET cc_start: 0.8385 (mmm) cc_final: 0.8057 (tpt) REVERT: B 673 LEU cc_start: 0.8010 (mm) cc_final: 0.7652 (mp) REVERT: B 699 ASP cc_start: 0.8298 (p0) cc_final: 0.8079 (p0) REVERT: B 702 ARG cc_start: 0.8559 (ppt90) cc_final: 0.8254 (mtt-85) REVERT: C 319 PHE cc_start: 0.8650 (t80) cc_final: 0.8319 (t80) REVERT: C 323 MET cc_start: 0.8394 (ttp) cc_final: 0.8100 (mtm) REVERT: C 530 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: C 540 PHE cc_start: 0.8203 (t80) cc_final: 0.7968 (t80) REVERT: C 552 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8507 (mmt-90) REVERT: C 615 LEU cc_start: 0.9027 (mt) cc_final: 0.8778 (mp) REVERT: C 661 HIS cc_start: 0.8016 (m-70) cc_final: 0.6964 (m90) REVERT: D 64 TRP cc_start: 0.8427 (m100) cc_final: 0.7773 (m-10) REVERT: D 70 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6711 (tmt) REVERT: D 126 TYR cc_start: 0.7544 (m-10) cc_final: 0.7344 (m-10) REVERT: D 369 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7901 (mtm180) REVERT: D 432 GLU cc_start: 0.8233 (tt0) cc_final: 0.7804 (tt0) REVERT: D 481 ASP cc_start: 0.7720 (p0) cc_final: 0.7425 (t0) REVERT: D 493 PHE cc_start: 0.8105 (p90) cc_final: 0.7563 (p90) REVERT: D 494 HIS cc_start: 0.8073 (m170) cc_final: 0.7812 (m-70) REVERT: D 543 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7653 (p0) REVERT: D 645 LYS cc_start: 0.9092 (tptp) cc_final: 0.8542 (mtmm) REVERT: D 666 HIS cc_start: 0.7008 (m-70) cc_final: 0.6212 (m-70) REVERT: D 671 GLU cc_start: 0.8779 (tp30) cc_final: 0.8152 (tp30) REVERT: D 673 LEU cc_start: 0.7666 (mt) cc_final: 0.6990 (mt) REVERT: D 702 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7739 (mtm-85) outliers start: 60 outliers final: 42 residues processed: 259 average time/residue: 0.5335 time to fit residues: 160.8677 Evaluate side-chains 258 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 5 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 179 optimal weight: 5.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.156443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097957 restraints weight = 31747.385| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.21 r_work: 0.3147 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22552 Z= 0.128 Angle : 0.690 19.713 30484 Z= 0.339 Chirality : 0.043 0.186 3364 Planarity : 0.004 0.077 3854 Dihedral : 5.062 25.438 2992 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.13 % Favored : 91.83 % Rotamer: Outliers : 2.08 % Allowed : 22.04 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2706 helix: -0.34 (0.14), residues: 1530 sheet: -1.59 (0.45), residues: 135 loop : -1.15 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 702 TYR 0.029 0.001 TYR B 120 PHE 0.031 0.001 PHE A 540 TRP 0.012 0.001 TRP C 64 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (22552) covalent geometry : angle 0.69038 / 0.34 (30484) hydrogen bonds : bond 0.03306 / 2.07 ( 898) hydrogen bonds : angle 4.00281 / 2.78 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8896.91 seconds wall clock time: 152 minutes 13.65 seconds (9133.65 seconds total)