Starting phenix.real_space_refine on Fri Sep 19 01:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0x_61061/09_2025/9j0x_61061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0x_61061/09_2025/9j0x_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_61061/09_2025/9j0x_61061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0x_61061/09_2025/9j0x_61061.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0x_61061/09_2025/9j0x_61061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0x_61061/09_2025/9j0x_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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.27 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: 1.84 Conformation dependent library (CDL) restraints added in 984.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.90 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: 3.90 Time building geometry restraints manager: 2.47 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 21.480 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 aren 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 covalent geometry : bond 0.00524 (22552) covalent geometry : angle 1.02711 (30484) hydrogen bonds : bond 0.17502 ( 898) hydrogen bonds : angle 7.09324 ( 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 : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.6732 time to fit residues: 292.6272 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 : 0.884 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 278 HIS A 396 ASN A 416 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.155906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098622 restraints weight = 31978.781| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.17 r_work: 0.3139 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22552 Z= 0.154 Angle : 0.669 14.836 30484 Z= 0.346 Chirality : 0.043 0.198 3364 Planarity : 0.005 0.051 3854 Dihedral : 6.186 87.833 2994 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 2.54 % Allowed : 14.83 % 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 aren not related in a simple way. whole: -3.18 (0.14), residues: 2706 helix: -2.01 (0.11), residues: 1504 sheet: -2.00 (0.45), residues: 119 loop : -2.05 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 552 TYR 0.020 0.001 TYR C 492 PHE 0.020 0.001 PHE A 623 TRP 0.016 0.001 TRP C 255 HIS 0.008 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00348 (22552) covalent geometry : angle 0.66947 (30484) hydrogen bonds : bond 0.04030 ( 898) hydrogen bonds : angle 4.65221 ( 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 327 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.882 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: 0.7429 (tmt170) cc_final: 0.5689 (ptt180) REVERT: A 320 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7458 (ttm110) REVERT: A 337 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: A 340 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7954 (mtp85) REVERT: A 470 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7698 (mtp-110) REVERT: A 483 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8513 (tp-100) REVERT: B 37 TRP cc_start: 0.6227 (m100) cc_final: 0.5959 (m100) REVERT: B 63 ARG cc_start: 0.7468 (tmm-80) cc_final: 0.6528 (tmm160) REVERT: B 121 ARG cc_start: 0.7774 (tpm170) cc_final: 0.7229 (tpp-160) REVERT: B 137 PHE cc_start: 0.7786 (m-80) cc_final: 0.7251 (m-10) REVERT: B 301 TYR cc_start: 0.8105 (t80) cc_final: 0.7527 (m-80) REVERT: B 317 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: B 493 PHE cc_start: 0.8537 (p90) cc_final: 0.8268 (p90) REVERT: B 546 GLN cc_start: 0.9240 (tp-100) cc_final: 0.8581 (tp-100) REVERT: B 666 HIS cc_start: 0.7254 (t70) cc_final: 0.6144 (t-170) REVERT: B 698 LEU cc_start: 0.9285 (tt) cc_final: 0.8955 (mp) REVERT: C 316 THR cc_start: 0.9476 (t) cc_final: 0.9211 (t) REVERT: C 317 GLU cc_start: 0.8037 (pm20) cc_final: 0.7795 (mp0) REVERT: C 479 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7609 (ttp80) REVERT: C 504 MET cc_start: 0.7490 (tpp) cc_final: 0.7214 (mmt) REVERT: C 615 LEU cc_start: 0.9088 (mt) cc_final: 0.8880 (mp) REVERT: C 618 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8877 (mmpt) REVERT: D 51 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.5665 (t70) REVERT: D 355 TYR cc_start: 0.6139 (t80) cc_final: 0.5813 (t80) REVERT: D 369 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7737 (mtm180) REVERT: D 432 GLU cc_start: 0.8222 (tt0) cc_final: 0.7639 (tt0) REVERT: D 661 HIS cc_start: 0.8020 (m90) cc_final: 0.7656 (m170) REVERT: D 666 HIS cc_start: 0.7168 (m-70) cc_final: 0.6382 (m-70) REVERT: D 671 GLU cc_start: 0.8784 (tp30) cc_final: 0.8237 (tp30) REVERT: D 673 LEU cc_start: 0.7938 (mt) cc_final: 0.7449 (mt) outliers start: 61 outliers final: 14 residues processed: 305 average time/residue: 0.6057 time to fit residues: 212.2182 Evaluate side-chains 231 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 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: 0.8980 chunk 207 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 114 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS B 350 GLN B 354 HIS B 527 GLN B 558 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN D 510 ASN D 591 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.158476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100189 restraints weight = 32165.398| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.29 r_work: 0.3148 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22552 Z= 0.123 Angle : 0.627 15.044 30484 Z= 0.321 Chirality : 0.042 0.266 3364 Planarity : 0.004 0.047 3854 Dihedral : 5.491 25.494 2992 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 2.92 % Allowed : 16.38 % Favored : 80.71 % 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 aren not related in a simple way. whole: -2.28 (0.16), residues: 2706 helix: -1.21 (0.13), residues: 1500 sheet: -1.66 (0.47), residues: 120 loop : -1.76 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 662 TYR 0.017 0.001 TYR B 562 PHE 0.021 0.001 PHE C 540 TRP 0.012 0.001 TRP C 255 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00272 (22552) covalent geometry : angle 0.62715 (30484) hydrogen bonds : bond 0.03459 ( 898) hydrogen bonds : angle 4.14871 ( 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 310 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7479 (tmt170) cc_final: 0.5739 (ptt180) REVERT: A 206 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6978 (t80) REVERT: A 320 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7466 (ttm110) REVERT: A 326 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 337 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.8009 (tpp-160) REVERT: A 340 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7998 (mtm-85) REVERT: A 430 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8160 (tm) REVERT: A 470 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7665 (mtp-110) REVERT: A 483 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8570 (tp40) REVERT: A 623 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: B 37 TRP cc_start: 0.6030 (m100) cc_final: 0.5804 (m100) REVERT: B 63 ARG cc_start: 0.7483 (tmm-80) cc_final: 0.6604 (tmm160) REVERT: B 121 ARG cc_start: 0.7647 (tpm170) cc_final: 0.7094 (tpp-160) REVERT: B 137 PHE cc_start: 0.7791 (m-80) cc_final: 0.7150 (m-10) REVERT: B 301 TYR cc_start: 0.8075 (t80) cc_final: 0.7535 (m-80) REVERT: B 317 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: B 323 MET cc_start: 0.8524 (tpt) cc_final: 0.8316 (tpp) REVERT: B 546 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8459 (tp-100) REVERT: B 558 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6182 (m-40) REVERT: B 652 MET cc_start: 0.8231 (mmm) cc_final: 0.7870 (tpt) REVERT: B 665 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7389 (tm) REVERT: B 666 HIS cc_start: 0.7587 (t70) cc_final: 0.6403 (t-170) REVERT: B 698 LEU cc_start: 0.9150 (tt) cc_final: 0.8894 (mp) REVERT: C 316 THR cc_start: 0.9455 (t) cc_final: 0.9105 (t) REVERT: C 317 GLU cc_start: 0.8119 (pm20) cc_final: 0.7886 (mp0) REVERT: C 351 TYR cc_start: 0.8770 (t80) cc_final: 0.8563 (t80) REVERT: C 405 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7790 (mt-10) REVERT: C 479 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: C 574 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8469 (mmm-85) REVERT: C 615 LEU cc_start: 0.9021 (mt) cc_final: 0.8814 (mp) REVERT: C 618 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8838 (mmpt) REVERT: C 676 MET cc_start: 0.8592 (mmt) cc_final: 0.8317 (mmt) REVERT: D 51 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.6037 (t70) REVERT: D 70 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6401 (tmm) REVERT: D 369 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7849 (mtm180) REVERT: D 432 GLU cc_start: 0.8223 (tt0) cc_final: 0.7690 (tt0) REVERT: D 493 PHE cc_start: 0.8171 (p90) cc_final: 0.7633 (p90) REVERT: D 661 HIS cc_start: 0.7987 (m90) cc_final: 0.7631 (m170) REVERT: D 666 HIS cc_start: 0.7012 (m-70) cc_final: 0.6273 (m-70) REVERT: D 671 GLU cc_start: 0.8842 (tp30) cc_final: 0.8275 (tp30) REVERT: D 673 LEU cc_start: 0.7910 (mt) cc_final: 0.7398 (mt) REVERT: D 702 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8041 (mtm180) outliers start: 70 outliers final: 18 residues processed: 290 average time/residue: 0.5953 time to fit residues: 200.1434 Evaluate side-chains 245 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU 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 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 558 ASN 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 613 ILE Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 503 ILE 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 202 LEU 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: 1.9990 chunk 252 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 483 GLN A 591 ASN B 350 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 HIS D 609 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.151634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092740 restraints weight = 32200.462| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.31 r_work: 0.3045 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22552 Z= 0.259 Angle : 0.697 14.343 30484 Z= 0.357 Chirality : 0.047 0.342 3364 Planarity : 0.004 0.047 3854 Dihedral : 5.627 25.929 2992 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer: Outliers : 3.71 % Allowed : 16.83 % Favored : 79.46 % 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 aren not related in a simple way. whole: -2.12 (0.16), residues: 2706 helix: -1.07 (0.13), residues: 1529 sheet: -1.87 (0.45), residues: 129 loop : -1.65 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 662 TYR 0.018 0.002 TYR D 210 PHE 0.021 0.002 PHE D 544 TRP 0.017 0.002 TRP C 255 HIS 0.010 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00617 (22552) covalent geometry : angle 0.69680 (30484) hydrogen bonds : bond 0.04032 ( 898) hydrogen bonds : angle 4.28385 ( 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 319 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7625 (tmt170) cc_final: 0.5712 (ptt180) REVERT: A 193 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6929 (mtm-85) REVERT: A 206 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 320 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7511 (ttm110) REVERT: A 337 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.7936 (tpp-160) REVERT: A 470 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7654 (mtp-110) REVERT: A 483 GLN cc_start: 0.8858 (tp40) cc_final: 0.8592 (tp40) REVERT: A 623 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: B 37 TRP cc_start: 0.6128 (m100) cc_final: 0.5873 (m100) REVERT: B 63 ARG cc_start: 0.7536 (tmm-80) cc_final: 0.6570 (tmm160) REVERT: B 121 ARG cc_start: 0.7777 (tpm170) cc_final: 0.7332 (tpt170) REVERT: B 137 PHE cc_start: 0.7881 (m-80) cc_final: 0.7255 (m-10) REVERT: B 204 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8047 (mm) REVERT: B 301 TYR cc_start: 0.8214 (t80) cc_final: 0.7612 (m-80) REVERT: B 317 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: B 493 PHE cc_start: 0.8670 (p90) cc_final: 0.8398 (p90) REVERT: B 546 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8529 (tp-100) REVERT: B 642 ASP cc_start: 0.8745 (p0) cc_final: 0.8455 (p0) REVERT: B 665 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 666 HIS cc_start: 0.7255 (t70) cc_final: 0.6152 (t-170) REVERT: B 698 LEU cc_start: 0.9179 (tt) cc_final: 0.8918 (mp) REVERT: C 317 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: C 405 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 479 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: C 530 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: C 540 PHE cc_start: 0.8560 (t80) cc_final: 0.8330 (t80) REVERT: C 552 ARG cc_start: 0.8879 (mtt90) cc_final: 0.8207 (mpt90) REVERT: C 615 LEU cc_start: 0.9040 (mt) cc_final: 0.8798 (mp) REVERT: C 618 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8883 (mmpt) REVERT: C 661 HIS cc_start: 0.8023 (m-70) cc_final: 0.6975 (m90) REVERT: D 51 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.6060 (t70) REVERT: D 70 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6699 (tmt) REVERT: D 113 VAL cc_start: 0.8640 (p) cc_final: 0.8388 (t) REVERT: D 369 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7818 (mtm180) REVERT: D 432 GLU cc_start: 0.8230 (tt0) cc_final: 0.7668 (tt0) REVERT: D 436 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7350 (t) REVERT: D 520 ILE cc_start: 0.5653 (OUTLIER) cc_final: 0.5452 (pp) REVERT: D 666 HIS cc_start: 0.7139 (m-70) cc_final: 0.6327 (m-70) REVERT: D 671 GLU cc_start: 0.8814 (tp30) cc_final: 0.8285 (tp30) REVERT: D 673 LEU cc_start: 0.8002 (mt) cc_final: 0.7557 (mt) REVERT: D 702 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7980 (mtm-85) REVERT: D 710 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7733 (mp) outliers start: 89 outliers final: 34 residues processed: 294 average time/residue: 0.5986 time to fit residues: 203.7742 Evaluate side-chains 256 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 309 LEU Chi-restraints excluded: chain A residue 354 HIS 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 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 125 THR 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 605 VAL Chi-restraints excluded: chain B residue 613 ILE 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 704 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 354 HIS 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 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 167 optimal weight: 0.4980 chunk 225 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097682 restraints weight = 31780.026| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.25 r_work: 0.3126 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22552 Z= 0.121 Angle : 0.632 16.680 30484 Z= 0.318 Chirality : 0.042 0.309 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.308 25.275 2992 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 2.71 % Allowed : 18.38 % 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 aren not related in a simple way. whole: -1.71 (0.16), residues: 2706 helix: -0.70 (0.13), residues: 1500 sheet: -1.64 (0.46), residues: 130 loop : -1.53 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 193 TYR 0.018 0.001 TYR D 355 PHE 0.016 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 covalent geometry : bond 0.00272 (22552) covalent geometry : angle 0.63240 (30484) hydrogen bonds : bond 0.03280 ( 898) hydrogen bonds : angle 3.96816 ( 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 297 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8847 (mmp) cc_final: 0.8504 (mmm) REVERT: A 96 ARG cc_start: 0.7627 (tmt170) cc_final: 0.5801 (ptt180) REVERT: A 193 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6838 (mtm-85) REVERT: A 206 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 320 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7449 (ttm110) REVERT: A 337 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.7963 (tpp-160) REVERT: A 408 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 470 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7707 (mtp-110) REVERT: A 483 GLN cc_start: 0.8938 (tp40) cc_final: 0.8642 (tp40) REVERT: A 623 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: B 37 TRP cc_start: 0.6025 (m100) cc_final: 0.5774 (m100) REVERT: B 63 ARG cc_start: 0.7552 (tmm-80) cc_final: 0.6539 (tmm160) REVERT: B 121 ARG cc_start: 0.7548 (tpm170) cc_final: 0.6763 (tpp-160) REVERT: B 137 PHE cc_start: 0.7798 (m-80) cc_final: 0.7168 (m-10) REVERT: B 204 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7979 (mm) REVERT: B 301 TYR cc_start: 0.8092 (t80) cc_final: 0.7562 (m-80) REVERT: B 317 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: B 493 PHE cc_start: 0.8690 (p90) cc_final: 0.8435 (p90) REVERT: B 520 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6155 (mp) REVERT: B 546 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8459 (tp-100) REVERT: B 642 ASP cc_start: 0.8715 (p0) cc_final: 0.8395 (p0) REVERT: B 652 MET cc_start: 0.8245 (mmm) cc_final: 0.7749 (tpt) REVERT: B 665 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 666 HIS cc_start: 0.7336 (t70) cc_final: 0.6374 (t-170) REVERT: B 673 LEU cc_start: 0.7965 (mm) cc_final: 0.7558 (mp) REVERT: B 698 LEU cc_start: 0.9026 (tt) cc_final: 0.8822 (mp) REVERT: C 403 HIS cc_start: 0.7649 (m90) cc_final: 0.7257 (m-70) REVERT: C 405 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7735 (mt-10) REVERT: C 479 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7314 (mtm-85) REVERT: C 505 GLU cc_start: 0.8039 (pp20) cc_final: 0.7826 (pp20) REVERT: C 530 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: C 552 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8612 (mmt-90) REVERT: C 615 LEU cc_start: 0.9027 (mt) cc_final: 0.8764 (mp) REVERT: C 618 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8870 (mmpt) REVERT: C 661 HIS cc_start: 0.8066 (m-70) cc_final: 0.6971 (m90) REVERT: C 676 MET cc_start: 0.8316 (mmt) cc_final: 0.8100 (mmt) REVERT: D 51 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.6088 (t70) REVERT: D 70 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6474 (tmt) REVERT: D 369 ARG cc_start: 0.8085 (mtm110) cc_final: 0.7849 (mtm180) REVERT: D 432 GLU cc_start: 0.8207 (tt0) cc_final: 0.7710 (tt0) REVERT: D 481 ASP cc_start: 0.7726 (p0) cc_final: 0.7447 (t0) REVERT: D 524 ILE cc_start: 0.2970 (OUTLIER) cc_final: 0.2686 (mp) REVERT: D 642 ASP cc_start: 0.8699 (m-30) cc_final: 0.8344 (m-30) REVERT: D 645 LYS cc_start: 0.9147 (tptp) cc_final: 0.8657 (mtmm) REVERT: D 666 HIS cc_start: 0.7025 (m-70) cc_final: 0.6271 (m-70) REVERT: D 671 GLU cc_start: 0.8763 (tp30) cc_final: 0.8163 (tp30) REVERT: D 673 LEU cc_start: 0.7848 (mt) cc_final: 0.7270 (mt) REVERT: D 702 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7600 (mtt-85) REVERT: D 710 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7705 (mp) outliers start: 65 outliers final: 17 residues processed: 280 average time/residue: 0.5694 time to fit residues: 185.2082 Evaluate side-chains 241 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 490 GLU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain B residue 133 THR 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 520 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 613 ILE Chi-restraints excluded: chain B residue 665 LEU 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 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 524 ILE Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 62 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095658 restraints weight = 32166.993| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.27 r_work: 0.3103 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22552 Z= 0.151 Angle : 0.643 17.206 30484 Z= 0.323 Chirality : 0.043 0.346 3364 Planarity : 0.004 0.048 3854 Dihedral : 5.223 25.429 2992 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.43 % Favored : 91.54 % Rotamer: Outliers : 3.04 % Allowed : 18.62 % Favored : 78.33 % 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 aren not related in a simple way. whole: -1.53 (0.16), residues: 2706 helix: -0.57 (0.14), residues: 1503 sheet: -1.58 (0.46), residues: 130 loop : -1.43 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 552 TYR 0.018 0.001 TYR C 492 PHE 0.041 0.001 PHE C 540 TRP 0.013 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00353 (22552) covalent geometry : angle 0.64308 (30484) hydrogen bonds : bond 0.03417 ( 898) hydrogen bonds : angle 3.98939 ( 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 304 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 231 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8898 (mmp) cc_final: 0.8535 (mmm) REVERT: A 96 ARG cc_start: 0.7628 (tmt170) cc_final: 0.5782 (ptt180) REVERT: A 193 ARG cc_start: 0.7097 (mtm180) cc_final: 0.6868 (mtm-85) REVERT: A 206 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 320 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7493 (ttm110) REVERT: A 337 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.7942 (tpp-160) REVERT: A 408 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 470 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7677 (mtp-110) REVERT: A 483 GLN cc_start: 0.8942 (tp40) cc_final: 0.8629 (tp40) REVERT: A 623 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: B 37 TRP cc_start: 0.6056 (m100) cc_final: 0.5811 (m100) REVERT: B 63 ARG cc_start: 0.7555 (tmm-80) cc_final: 0.6548 (tmm160) REVERT: B 121 ARG cc_start: 0.7570 (tpm170) cc_final: 0.6770 (tpp-160) REVERT: B 137 PHE cc_start: 0.7807 (m-80) cc_final: 0.7174 (m-10) REVERT: B 204 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 301 TYR cc_start: 0.8109 (t80) cc_final: 0.7538 (m-80) REVERT: B 317 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: B 360 MET cc_start: 0.9121 (ppp) cc_final: 0.8602 (ppp) REVERT: B 493 PHE cc_start: 0.8706 (p90) cc_final: 0.8376 (p90) REVERT: B 546 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8415 (tp-100) REVERT: B 552 ARG cc_start: 0.8298 (mmp80) cc_final: 0.8069 (mmp80) REVERT: B 610 GLU cc_start: 0.7017 (pm20) cc_final: 0.6784 (mp0) REVERT: B 642 ASP cc_start: 0.8737 (p0) cc_final: 0.8430 (p0) REVERT: B 652 MET cc_start: 0.8278 (mmm) cc_final: 0.7755 (tpt) REVERT: B 665 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7415 (tt) REVERT: B 673 LEU cc_start: 0.7968 (mm) cc_final: 0.7632 (mp) REVERT: B 675 LEU cc_start: 0.8485 (tm) cc_final: 0.8266 (pp) REVERT: B 702 ARG cc_start: 0.8606 (ppt90) cc_final: 0.8345 (mtt-85) REVERT: C 403 HIS cc_start: 0.7681 (m90) cc_final: 0.7267 (m-70) REVERT: C 405 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 479 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7342 (mtm-85) REVERT: C 483 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 505 GLU cc_start: 0.8125 (pp20) cc_final: 0.7886 (pp20) REVERT: C 530 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: C 552 ARG cc_start: 0.8935 (mtt90) cc_final: 0.8621 (mmt-90) REVERT: C 574 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8401 (mmm-85) REVERT: C 615 LEU cc_start: 0.8994 (mt) cc_final: 0.8712 (mp) REVERT: C 618 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8889 (mmpt) REVERT: C 661 HIS cc_start: 0.8060 (m-70) cc_final: 0.6989 (m90) REVERT: D 70 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6566 (tmt) REVERT: D 337 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7858 (ptm-80) REVERT: D 369 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7870 (mtm180) REVERT: D 432 GLU cc_start: 0.8210 (tt0) cc_final: 0.7676 (tt0) REVERT: D 481 ASP cc_start: 0.7728 (p0) cc_final: 0.7427 (t0) REVERT: D 524 ILE cc_start: 0.3367 (OUTLIER) cc_final: 0.3142 (mp) REVERT: D 544 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: D 545 TYR cc_start: 0.8636 (m-80) cc_final: 0.8359 (m-80) REVERT: D 642 ASP cc_start: 0.8768 (m-30) cc_final: 0.8467 (m-30) REVERT: D 645 LYS cc_start: 0.9176 (tptp) cc_final: 0.8531 (mtmm) REVERT: D 666 HIS cc_start: 0.6995 (m-70) cc_final: 0.6198 (m-70) REVERT: D 671 GLU cc_start: 0.8801 (tp30) cc_final: 0.8185 (tp30) REVERT: D 673 LEU cc_start: 0.7793 (mt) cc_final: 0.7205 (mt) REVERT: D 702 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7948 (mtm-85) REVERT: D 710 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7538 (pp) outliers start: 73 outliers final: 26 residues processed: 282 average time/residue: 0.5753 time to fit residues: 186.8438 Evaluate side-chains 256 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 448 LEU 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 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 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 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 704 CYS 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 479 ARG Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 710 ILE 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: 0.0870 chunk 57 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 221 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 591 ASN ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.156235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097798 restraints weight = 31629.827| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.32 r_work: 0.3135 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3114 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= 0.127 Angle : 0.647 18.081 30484 Z= 0.320 Chirality : 0.042 0.372 3364 Planarity : 0.004 0.053 3854 Dihedral : 5.110 25.058 2992 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 2.58 % Allowed : 19.58 % Favored : 77.83 % 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 aren not related in a simple way. whole: -1.37 (0.16), residues: 2706 helix: -0.44 (0.14), residues: 1509 sheet: -1.52 (0.46), residues: 130 loop : -1.35 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 552 TYR 0.019 0.001 TYR D 355 PHE 0.020 0.001 PHE A 540 TRP 0.011 0.001 TRP C 255 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00291 (22552) covalent geometry : angle 0.64708 (30484) hydrogen bonds : bond 0.03211 ( 898) hydrogen bonds : angle 3.90714 ( 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 292 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8835 (mmp) cc_final: 0.8479 (mmm) REVERT: A 96 ARG cc_start: 0.7563 (tmt170) cc_final: 0.5776 (ptt180) REVERT: A 193 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6841 (mtm-85) REVERT: A 320 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7498 (ttm110) REVERT: A 337 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.7929 (tpp-160) REVERT: A 430 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8094 (tm) REVERT: A 470 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7682 (mtp-110) REVERT: A 483 GLN cc_start: 0.8898 (tp40) cc_final: 0.8563 (tp40) REVERT: A 623 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: B 37 TRP cc_start: 0.5829 (m100) cc_final: 0.5609 (m100) REVERT: B 63 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.6563 (tmm160) REVERT: B 121 ARG cc_start: 0.7451 (tpm170) cc_final: 0.6885 (tpp-160) REVERT: B 137 PHE cc_start: 0.7786 (m-80) cc_final: 0.7149 (m-10) REVERT: B 204 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8065 (mm) REVERT: B 317 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: B 360 MET cc_start: 0.9104 (ppp) cc_final: 0.8640 (ppp) REVERT: B 493 PHE cc_start: 0.8747 (p90) cc_final: 0.8420 (p90) REVERT: B 546 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8365 (tp-100) REVERT: B 552 ARG cc_start: 0.8398 (mmp80) cc_final: 0.8087 (mmp80) REVERT: B 642 ASP cc_start: 0.8750 (p0) cc_final: 0.8443 (p0) REVERT: B 673 LEU cc_start: 0.7995 (mm) cc_final: 0.7695 (mp) REVERT: B 675 LEU cc_start: 0.8462 (tm) cc_final: 0.8251 (pp) REVERT: B 699 ASP cc_start: 0.8336 (p0) cc_final: 0.8131 (p0) REVERT: C 323 MET cc_start: 0.8362 (ttp) cc_final: 0.8107 (mtm) REVERT: C 403 HIS cc_start: 0.7714 (m90) cc_final: 0.7313 (m-70) REVERT: C 405 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7768 (mt-10) REVERT: C 479 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7386 (mtm-85) REVERT: C 483 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 530 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 552 ARG cc_start: 0.8909 (mtt90) cc_final: 0.8598 (mmt-90) REVERT: C 615 LEU cc_start: 0.9020 (mt) cc_final: 0.8743 (mp) REVERT: C 618 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8869 (mmpt) REVERT: C 661 HIS cc_start: 0.8028 (m-70) cc_final: 0.6962 (m90) REVERT: D 64 TRP cc_start: 0.8444 (m100) cc_final: 0.7691 (m-10) REVERT: D 70 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6585 (tmt) REVERT: D 369 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7821 (mtm180) REVERT: D 432 GLU cc_start: 0.8259 (tt0) cc_final: 0.7795 (tt0) REVERT: D 481 ASP cc_start: 0.7737 (p0) cc_final: 0.7498 (t0) REVERT: D 524 ILE cc_start: 0.3724 (OUTLIER) cc_final: 0.3392 (mp) REVERT: D 545 TYR cc_start: 0.8699 (m-80) cc_final: 0.8493 (m-80) REVERT: D 610 GLU cc_start: 0.7943 (pm20) cc_final: 0.7086 (tm-30) REVERT: D 642 ASP cc_start: 0.8807 (m-30) cc_final: 0.8570 (m-30) REVERT: D 645 LYS cc_start: 0.9059 (tptp) cc_final: 0.8533 (mtmm) REVERT: D 666 HIS cc_start: 0.7018 (m-70) cc_final: 0.6218 (m-70) REVERT: D 671 GLU cc_start: 0.8753 (tp30) cc_final: 0.8097 (tp30) REVERT: D 673 LEU cc_start: 0.7733 (mt) cc_final: 0.7046 (mt) REVERT: D 702 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7935 (mtm-85) REVERT: D 710 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7512 (pp) outliers start: 62 outliers final: 24 residues processed: 273 average time/residue: 0.5650 time to fit residues: 178.6006 Evaluate side-chains 249 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR 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 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 583 LEU 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 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 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 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 710 ILE 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: 0.9990 chunk 126 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098318 restraints weight = 31689.943| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.13 r_work: 0.3123 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3220 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= 0.143 Angle : 0.655 18.160 30484 Z= 0.326 Chirality : 0.044 0.378 3364 Planarity : 0.004 0.051 3854 Dihedral : 5.079 25.292 2992 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.35 % Favored : 91.61 % Rotamer: Outliers : 2.58 % Allowed : 20.12 % Favored : 77.29 % 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 aren not related in a simple way. whole: -1.35 (0.17), residues: 2706 helix: -0.44 (0.14), residues: 1524 sheet: -1.51 (0.46), residues: 130 loop : -1.33 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 552 TYR 0.016 0.001 TYR C 492 PHE 0.025 0.001 PHE A 540 TRP 0.011 0.001 TRP C 255 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00333 (22552) covalent geometry : angle 0.65529 (30484) hydrogen bonds : bond 0.03267 ( 898) hydrogen bonds : angle 3.90592 ( 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 288 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8818 (mmp) cc_final: 0.8486 (mmm) REVERT: A 96 ARG cc_start: 0.7605 (tmt170) cc_final: 0.5823 (ptt180) REVERT: A 193 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6870 (mtm-85) REVERT: A 320 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7546 (ttm110) REVERT: A 337 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.7930 (tpp-160) REVERT: A 408 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8426 (mm) REVERT: A 430 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8077 (tm) REVERT: A 470 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7712 (mtp-110) REVERT: A 483 GLN cc_start: 0.8931 (tp40) cc_final: 0.8618 (tp40) REVERT: A 623 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: B 37 TRP cc_start: 0.5825 (m100) cc_final: 0.5614 (m100) REVERT: B 63 ARG cc_start: 0.7601 (tmm-80) cc_final: 0.6608 (tmm160) REVERT: B 121 ARG cc_start: 0.7543 (tpm170) cc_final: 0.6959 (tpp-160) REVERT: B 137 PHE cc_start: 0.7825 (m-80) cc_final: 0.7197 (m-10) REVERT: B 204 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8088 (mm) REVERT: B 301 TYR cc_start: 0.8107 (t80) cc_final: 0.7600 (m-80) REVERT: B 317 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: B 360 MET cc_start: 0.9107 (ppp) cc_final: 0.8575 (ppp) REVERT: B 493 PHE cc_start: 0.8748 (p90) cc_final: 0.8489 (p90) REVERT: B 552 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8119 (mmp80) REVERT: B 642 ASP cc_start: 0.8746 (p0) cc_final: 0.8465 (p0) REVERT: B 645 LYS cc_start: 0.9197 (tppp) cc_final: 0.8974 (tmmt) REVERT: B 652 MET cc_start: 0.8288 (mmm) cc_final: 0.7929 (tpt) REVERT: B 673 LEU cc_start: 0.7941 (mm) cc_final: 0.7635 (mp) REVERT: B 702 ARG cc_start: 0.8546 (ppt90) cc_final: 0.8295 (mtt180) REVERT: C 194 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 319 PHE cc_start: 0.8680 (t80) cc_final: 0.8439 (t80) REVERT: C 323 MET cc_start: 0.8399 (ttp) cc_final: 0.8151 (mtm) REVERT: C 403 HIS cc_start: 0.7800 (m90) cc_final: 0.7386 (m-70) REVERT: C 405 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7794 (mt-10) REVERT: C 479 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7459 (mtm-85) REVERT: C 483 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 530 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: C 552 ARG cc_start: 0.8901 (mtt90) cc_final: 0.8607 (mmt-90) REVERT: C 615 LEU cc_start: 0.9023 (mt) cc_final: 0.8800 (mp) REVERT: C 661 HIS cc_start: 0.8038 (m-70) cc_final: 0.6981 (m90) REVERT: D 64 TRP cc_start: 0.8469 (m100) cc_final: 0.7778 (m-10) REVERT: D 70 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6731 (tmt) REVERT: D 112 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8113 (tp) REVERT: D 126 TYR cc_start: 0.7439 (m-10) cc_final: 0.7086 (m-10) REVERT: D 369 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7890 (mtm180) REVERT: D 432 GLU cc_start: 0.8271 (tt0) cc_final: 0.7824 (tt0) REVERT: D 481 ASP cc_start: 0.7752 (p0) cc_final: 0.7510 (t0) REVERT: D 543 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7432 (p0) REVERT: D 645 LYS cc_start: 0.9200 (tptp) cc_final: 0.8592 (mtmm) REVERT: D 666 HIS cc_start: 0.7024 (m-70) cc_final: 0.6209 (m-70) REVERT: D 671 GLU cc_start: 0.8775 (tp30) cc_final: 0.8140 (tp30) REVERT: D 673 LEU cc_start: 0.7710 (mt) cc_final: 0.7038 (mt) REVERT: D 702 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7969 (mtm-85) REVERT: D 710 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7690 (mp) outliers start: 62 outliers final: 29 residues processed: 268 average time/residue: 0.5792 time to fit residues: 179.3565 Evaluate side-chains 253 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 430 LEU 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 640 ASP 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 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 457 ILE 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 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 194 ILE 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 503 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 713 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099049 restraints weight = 31702.085| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.23 r_work: 0.3129 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22552 Z= 0.137 Angle : 0.672 18.527 30484 Z= 0.332 Chirality : 0.043 0.358 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.041 25.153 2992 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.39 % Favored : 91.57 % Rotamer: Outliers : 2.29 % Allowed : 21.00 % Favored : 76.71 % 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 aren not related in a simple way. whole: -1.24 (0.17), residues: 2706 helix: -0.33 (0.14), residues: 1518 sheet: -1.47 (0.46), residues: 130 loop : -1.30 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 552 TYR 0.023 0.001 TYR B 120 PHE 0.028 0.001 PHE A 540 TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00318 (22552) covalent geometry : angle 0.67182 (30484) hydrogen bonds : bond 0.03265 ( 898) hydrogen bonds : angle 3.92006 ( 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 279 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8817 (mmp) cc_final: 0.8483 (mmm) REVERT: A 96 ARG cc_start: 0.7601 (tmt170) cc_final: 0.5823 (ptt180) REVERT: A 193 ARG cc_start: 0.7048 (mtm180) cc_final: 0.6821 (mtm-85) REVERT: A 320 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7543 (ttm110) REVERT: A 337 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.7926 (tpp-160) REVERT: A 470 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7718 (mtp-110) REVERT: A 483 GLN cc_start: 0.8931 (tp40) cc_final: 0.8580 (tp40) REVERT: A 623 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: B 37 TRP cc_start: 0.5799 (m100) cc_final: 0.5574 (m100) REVERT: B 63 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.6575 (tmm160) REVERT: B 121 ARG cc_start: 0.7565 (tpm170) cc_final: 0.6947 (tpp-160) REVERT: B 137 PHE cc_start: 0.7791 (m-80) cc_final: 0.7194 (m-10) REVERT: B 204 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 317 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: B 360 MET cc_start: 0.9115 (ppp) cc_final: 0.8567 (ppp) REVERT: B 362 GLN cc_start: 0.8809 (pm20) cc_final: 0.8587 (pm20) REVERT: B 493 PHE cc_start: 0.8684 (p90) cc_final: 0.8413 (p90) REVERT: B 550 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 552 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8182 (mmp80) REVERT: B 642 ASP cc_start: 0.8710 (p0) cc_final: 0.8396 (p0) REVERT: B 652 MET cc_start: 0.8281 (mmm) cc_final: 0.8046 (tpt) REVERT: B 673 LEU cc_start: 0.7993 (mm) cc_final: 0.7685 (mp) REVERT: B 702 ARG cc_start: 0.8554 (ppt90) cc_final: 0.8339 (mtt-85) REVERT: C 194 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8049 (mp) REVERT: C 319 PHE cc_start: 0.8667 (t80) cc_final: 0.8347 (t80) REVERT: C 323 MET cc_start: 0.8371 (ttp) cc_final: 0.8094 (mtm) REVERT: C 403 HIS cc_start: 0.7809 (m90) cc_final: 0.7453 (m-70) REVERT: C 405 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 479 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7487 (mtm-85) REVERT: C 483 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 530 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: C 552 ARG cc_start: 0.8902 (mtt90) cc_final: 0.8608 (mmt-90) REVERT: C 615 LEU cc_start: 0.9027 (mt) cc_final: 0.8793 (mp) REVERT: D 64 TRP cc_start: 0.8455 (m100) cc_final: 0.7789 (m-10) REVERT: D 70 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6725 (tmt) REVERT: D 369 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7891 (mtm180) REVERT: D 432 GLU cc_start: 0.8318 (tt0) cc_final: 0.7873 (tt0) REVERT: D 481 ASP cc_start: 0.7748 (p0) cc_final: 0.7511 (t0) REVERT: D 543 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7533 (p0) REVERT: D 666 HIS cc_start: 0.7053 (m-70) cc_final: 0.6238 (m-70) REVERT: D 671 GLU cc_start: 0.8757 (tp30) cc_final: 0.8136 (tp30) REVERT: D 673 LEU cc_start: 0.7609 (mt) cc_final: 0.6888 (mt) REVERT: D 702 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: D 710 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7604 (pp) outliers start: 55 outliers final: 26 residues processed: 260 average time/residue: 0.5827 time to fit residues: 175.1903 Evaluate side-chains 245 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 503 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 640 ASP 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 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 583 LEU 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 194 ILE 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 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 713 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 chunk 248 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097127 restraints weight = 31833.882| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.23 r_work: 0.3102 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22552 Z= 0.173 Angle : 0.702 18.107 30484 Z= 0.348 Chirality : 0.045 0.319 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.119 25.488 2992 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.72 % Favored : 91.24 % Rotamer: Outliers : 2.29 % Allowed : 21.08 % Favored : 76.62 % 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 aren not related in a simple way. whole: -1.26 (0.17), residues: 2706 helix: -0.36 (0.14), residues: 1522 sheet: -1.57 (0.44), residues: 135 loop : -1.28 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 552 TYR 0.017 0.001 TYR C 492 PHE 0.031 0.002 PHE A 540 TRP 0.013 0.001 TRP C 255 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00410 (22552) covalent geometry : angle 0.70191 (30484) hydrogen bonds : bond 0.03482 ( 898) hydrogen bonds : angle 4.00987 ( 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 270 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8851 (mmp) cc_final: 0.8521 (mmm) REVERT: A 96 ARG cc_start: 0.7587 (tmt170) cc_final: 0.5794 (ptt180) REVERT: A 193 ARG cc_start: 0.7055 (mtm180) cc_final: 0.6825 (mtm-85) REVERT: A 320 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7548 (ttm110) REVERT: A 337 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.7915 (tpp-160) REVERT: A 470 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7704 (mtp-110) REVERT: A 483 GLN cc_start: 0.8933 (tp40) cc_final: 0.8555 (tp40) REVERT: A 623 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: B 37 TRP cc_start: 0.5839 (m100) cc_final: 0.5621 (m100) REVERT: B 63 ARG cc_start: 0.7609 (tmm-80) cc_final: 0.6595 (tmm160) REVERT: B 121 ARG cc_start: 0.7627 (tpm170) cc_final: 0.6856 (tpp-160) REVERT: B 137 PHE cc_start: 0.7809 (m-80) cc_final: 0.7218 (m-10) REVERT: B 204 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 301 TYR cc_start: 0.8115 (t80) cc_final: 0.7599 (m-80) REVERT: B 317 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: B 330 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8512 (mtm) REVERT: B 360 MET cc_start: 0.9104 (ppp) cc_final: 0.8554 (ppp) REVERT: B 362 GLN cc_start: 0.8880 (pm20) cc_final: 0.8661 (pm20) REVERT: B 550 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 552 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8102 (mmp80) REVERT: B 642 ASP cc_start: 0.8727 (p0) cc_final: 0.8419 (p0) REVERT: B 652 MET cc_start: 0.8313 (mmm) cc_final: 0.7989 (tpt) REVERT: B 673 LEU cc_start: 0.8055 (mm) cc_final: 0.7655 (mp) REVERT: B 702 ARG cc_start: 0.8599 (ppt90) cc_final: 0.8288 (mtt-85) REVERT: C 194 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8092 (mm) REVERT: C 210 TYR cc_start: 0.8171 (m-80) cc_final: 0.7932 (m-80) REVERT: C 319 PHE cc_start: 0.8654 (t80) cc_final: 0.8340 (t80) REVERT: C 323 MET cc_start: 0.8415 (ttp) cc_final: 0.8157 (mtm) REVERT: C 403 HIS cc_start: 0.7841 (m90) cc_final: 0.7473 (m-70) REVERT: C 405 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 479 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: C 483 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 530 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: C 552 ARG cc_start: 0.8876 (mtt90) cc_final: 0.8592 (mmt-90) REVERT: C 615 LEU cc_start: 0.9010 (mt) cc_final: 0.8775 (mp) REVERT: C 661 HIS cc_start: 0.8034 (m-70) cc_final: 0.7006 (m90) REVERT: C 693 TRP cc_start: 0.7196 (m100) cc_final: 0.6805 (m100) REVERT: D 64 TRP cc_start: 0.8460 (m100) cc_final: 0.7795 (m-10) REVERT: D 70 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6767 (tmt) REVERT: D 369 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7884 (mtm180) REVERT: D 432 GLU cc_start: 0.8304 (tt0) cc_final: 0.7818 (tt0) REVERT: D 481 ASP cc_start: 0.7736 (p0) cc_final: 0.7477 (t0) REVERT: D 543 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7707 (p0) REVERT: D 645 LYS cc_start: 0.9037 (tptp) cc_final: 0.8697 (mtmm) REVERT: D 666 HIS cc_start: 0.7012 (m-70) cc_final: 0.6229 (m-70) REVERT: D 671 GLU cc_start: 0.8785 (tp30) cc_final: 0.8157 (tp30) REVERT: D 673 LEU cc_start: 0.7720 (mt) cc_final: 0.7046 (mt) REVERT: D 702 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: D 710 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7554 (pp) outliers start: 55 outliers final: 36 residues processed: 254 average time/residue: 0.5864 time to fit residues: 171.5315 Evaluate side-chains 251 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 581 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 640 ASP 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 317 GLU Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 550 LEU 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 704 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 316 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 202 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 398 ILE 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 599 THR Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 713 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 5 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097676 restraints weight = 31686.882| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.27 r_work: 0.3122 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22552 Z= 0.143 Angle : 0.694 18.363 30484 Z= 0.341 Chirality : 0.044 0.337 3364 Planarity : 0.004 0.048 3854 Dihedral : 5.059 25.473 2992 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.39 % Favored : 91.57 % Rotamer: Outliers : 2.17 % Allowed : 21.46 % 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 aren not related in a simple way. whole: -1.17 (0.17), residues: 2706 helix: -0.30 (0.14), residues: 1528 sheet: -1.54 (0.44), residues: 135 loop : -1.22 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 552 TYR 0.031 0.001 TYR D 545 PHE 0.030 0.001 PHE A 540 TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00332 (22552) covalent geometry : angle 0.69398 (30484) hydrogen bonds : bond 0.03326 ( 898) hydrogen bonds : angle 3.97111 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9684.36 seconds wall clock time: 165 minutes 16.48 seconds (9916.48 seconds total)