Starting phenix.real_space_refine on Thu Jun 19 03:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0x_61061/06_2025/9j0x_61061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0x_61061/06_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_61061/06_2025/9j0x_61061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0x_61061/06_2025/9j0x_61061.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0x_61061/06_2025/9j0x_61061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0x_61061/06_2025/9j0x_61061.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.14, per 1000 atoms: 0.60 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: 5.00 Conformation dependent library (CDL) restraints added in 2.8 seconds 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5096 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 16 sheets defined 56.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 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: 7.28 Time building geometry restraints manager: 6.02 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: 2.840 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: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 48.600 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP A 235 HIS 0.008 0.001 HIS C 666 PHE 0.020 0.002 PHE A 623 TYR 0.029 0.002 TYR B 562 ARG 0.007 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.17502 ( 898) hydrogen bonds : angle 7.09324 ( 2535) covalent geometry : bond 0.00524 (22552) covalent geometry : angle 1.02711 (30484) *********************** 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 : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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 408 LEU cc_start: 0.8986 (mt) cc_final: 0.8636 (mt) 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: 0.8188 (tp-100) REVERT: A 613 ILE cc_start: 0.8583 (mt) cc_final: 0.8378 (mp) REVERT: B 37 TRP cc_start: 0.6340 (m100) cc_final: 0.6048 (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 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 540 PHE cc_start: 0.8693 (t80) cc_final: 0.8452 (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: 0.7518 (m170) REVERT: D 645 LYS cc_start: 0.9083 (tmmt) cc_final: 0.8756 (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: 0.8096 (tp30) REVERT: D 673 LEU cc_start: 0.7881 (mt) cc_final: 0.7491 (mt) REVERT: D 702 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7919 (mtt-85) outliers start: 0 outliers final: 1 residues processed: 384 average time/residue: 1.3508 time to fit residues: 592.4127 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 : 2.706 ------------------------------------------------------------------------------- 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 226 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN A 416 GLN A 569 HIS A 624 ASN B 186 GLN B 346 HIS B 350 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097478 restraints weight = 32073.258| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.25 r_work: 0.3127 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22552 Z= 0.161 Angle : 0.668 15.314 30484 Z= 0.347 Chirality : 0.043 0.193 3364 Planarity : 0.005 0.051 3854 Dihedral : 6.196 87.654 2994 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.24 % Rotamer: Outliers : 2.50 % Allowed : 14.79 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.15), residues: 2706 helix: -2.00 (0.11), residues: 1505 sheet: -2.30 (0.43), residues: 127 loop : -2.03 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 255 HIS 0.005 0.001 HIS B 346 PHE 0.019 0.001 PHE A 623 TYR 0.021 0.001 TYR C 492 ARG 0.004 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 898) hydrogen bonds : angle 4.66356 ( 2535) covalent geometry : bond 0.00365 (22552) covalent geometry : angle 0.66827 (30484) *********************** 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 332 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 2.573 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: 0.7444 (tmt170) cc_final: 0.5739 (ptt180) REVERT: A 320 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7449 (ttm110) REVERT: A 326 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 337 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.7950 (tpp-160) REVERT: A 340 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7944 (mtp85) REVERT: A 470 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7695 (mtp-110) REVERT: A 483 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8622 (tp40) REVERT: A 490 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 523 HIS cc_start: 0.7715 (t-170) cc_final: 0.7331 (t-170) REVERT: A 666 HIS cc_start: 0.6299 (t-90) cc_final: 0.5340 (m170) REVERT: B 37 TRP cc_start: 0.6226 (m100) cc_final: 0.5958 (m100) REVERT: B 63 ARG cc_start: 0.7473 (tmm-80) cc_final: 0.6526 (tmm160) REVERT: B 121 ARG cc_start: 0.7790 (tpm170) cc_final: 0.7238 (tpp-160) REVERT: B 137 PHE cc_start: 0.7792 (m-80) cc_final: 0.7250 (m-10) REVERT: B 301 TYR cc_start: 0.8133 (t80) cc_final: 0.7558 (m-80) REVERT: B 317 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: B 388 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8282 (pttm) REVERT: B 493 PHE cc_start: 0.8554 (p90) cc_final: 0.8286 (p90) REVERT: B 546 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8586 (tp-100) REVERT: B 666 HIS cc_start: 0.7264 (t70) cc_final: 0.6169 (t-170) REVERT: C 316 THR cc_start: 0.9474 (t) cc_final: 0.9199 (t) REVERT: C 317 GLU cc_start: 0.8044 (pm20) cc_final: 0.7800 (mp0) REVERT: C 403 HIS cc_start: 0.7658 (m90) cc_final: 0.7307 (m-70) REVERT: C 405 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7975 (mt-10) REVERT: C 504 MET cc_start: 0.7484 (tpp) cc_final: 0.7232 (mmt) REVERT: C 615 LEU cc_start: 0.9088 (mt) cc_final: 0.8876 (mp) REVERT: C 618 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8895 (mmpt) REVERT: D 51 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5707 (t70) REVERT: D 355 TYR cc_start: 0.6143 (t80) cc_final: 0.5749 (t80) REVERT: D 369 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7747 (mtm180) REVERT: D 432 GLU cc_start: 0.8233 (tt0) cc_final: 0.7598 (tt0) REVERT: D 493 PHE cc_start: 0.8177 (p90) cc_final: 0.7698 (p90) REVERT: D 661 HIS cc_start: 0.8024 (m90) cc_final: 0.7664 (m170) REVERT: D 666 HIS cc_start: 0.7181 (m-70) cc_final: 0.6445 (m-70) REVERT: D 671 GLU cc_start: 0.8783 (tp30) cc_final: 0.8242 (tp30) REVERT: D 673 LEU cc_start: 0.7949 (mt) cc_final: 0.7456 (mt) outliers start: 60 outliers final: 11 residues processed: 310 average time/residue: 1.2985 time to fit residues: 467.8750 Evaluate side-chains 235 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 GLU 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 582 PHE Chi-restraints excluded: chain B residue 599 THR 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 161 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 350 GLN B 354 HIS B 374 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 HIS D 510 ASN ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095964 restraints weight = 32014.036| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.18 r_work: 0.3099 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22552 Z= 0.180 Angle : 0.659 14.967 30484 Z= 0.340 Chirality : 0.044 0.162 3364 Planarity : 0.004 0.047 3854 Dihedral : 5.655 25.595 2992 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.35 % Favored : 91.57 % Rotamer: Outliers : 3.29 % Allowed : 16.17 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2706 helix: -1.32 (0.13), residues: 1525 sheet: -1.74 (0.47), residues: 119 loop : -1.86 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 255 HIS 0.007 0.001 HIS D 494 PHE 0.019 0.002 PHE C 540 TYR 0.018 0.001 TYR A 258 ARG 0.009 0.001 ARG C 662 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 898) hydrogen bonds : angle 4.27786 ( 2535) covalent geometry : bond 0.00418 (22552) covalent geometry : angle 0.65938 (30484) *********************** 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 317 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 238 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7627 (tmt170) cc_final: 0.5790 (ptt180) REVERT: A 206 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7107 (t80) REVERT: A 320 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7465 (ttm110) REVERT: A 337 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.7997 (tpp-160) REVERT: A 340 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.8017 (mtp85) REVERT: A 430 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8175 (tm) REVERT: A 470 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7726 (mtp-110) REVERT: A 483 GLN cc_start: 0.8862 (tp40) cc_final: 0.8546 (tp40) REVERT: A 490 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 519 ASP cc_start: 0.8149 (t0) cc_final: 0.7766 (t70) REVERT: A 523 HIS cc_start: 0.7811 (t-170) cc_final: 0.7409 (t-170) REVERT: A 623 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 666 HIS cc_start: 0.6076 (t-90) cc_final: 0.5286 (m170) REVERT: B 37 TRP cc_start: 0.6179 (m100) cc_final: 0.5883 (m100) REVERT: B 63 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.6590 (tmm160) REVERT: B 121 ARG cc_start: 0.7760 (tpm170) cc_final: 0.7130 (tpp-160) REVERT: B 137 PHE cc_start: 0.7888 (m-80) cc_final: 0.7284 (m-10) REVERT: B 204 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7991 (mm) REVERT: B 301 TYR cc_start: 0.8156 (t80) cc_final: 0.7581 (m-80) REVERT: B 317 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: B 388 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8411 (mttp) REVERT: B 546 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8513 (tp-100) REVERT: B 652 MET cc_start: 0.8303 (mmm) cc_final: 0.7926 (tpt) REVERT: B 666 HIS cc_start: 0.7392 (t70) cc_final: 0.6249 (t-170) REVERT: B 698 LEU cc_start: 0.9172 (tt) cc_final: 0.8902 (mp) REVERT: C 316 THR cc_start: 0.9456 (t) cc_final: 0.9098 (t) REVERT: C 317 GLU cc_start: 0.8102 (pm20) cc_final: 0.7883 (mp0) REVERT: C 403 HIS cc_start: 0.7698 (m90) cc_final: 0.7355 (m-70) REVERT: C 405 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 479 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7103 (mtm-85) REVERT: C 504 MET cc_start: 0.7580 (tpp) cc_final: 0.7212 (mmt) REVERT: C 574 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8437 (mmm-85) REVERT: C 615 LEU cc_start: 0.9025 (mt) cc_final: 0.8802 (mp) REVERT: C 618 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8867 (mmpt) REVERT: C 661 HIS cc_start: 0.8002 (m-70) cc_final: 0.6908 (m90) REVERT: D 51 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.6121 (t70) REVERT: D 70 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6601 (tmm) REVERT: D 369 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7841 (mtm180) REVERT: D 432 GLU cc_start: 0.8215 (tt0) cc_final: 0.7629 (tt0) REVERT: D 661 HIS cc_start: 0.7966 (m90) cc_final: 0.7637 (m170) REVERT: D 666 HIS cc_start: 0.7162 (m-70) cc_final: 0.6405 (m-70) REVERT: D 671 GLU cc_start: 0.8808 (tp30) cc_final: 0.8255 (tp30) REVERT: D 673 LEU cc_start: 0.7987 (mt) cc_final: 0.7493 (mt) REVERT: D 702 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8045 (mtm-85) outliers start: 79 outliers final: 25 residues processed: 297 average time/residue: 1.1064 time to fit residues: 383.6105 Evaluate side-chains 253 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE 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 B residue 133 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 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 625 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 469 VAL 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 244 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 B 350 GLN B 527 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.154077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095810 restraints weight = 32228.694| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.27 r_work: 0.3091 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22552 Z= 0.165 Angle : 0.640 16.052 30484 Z= 0.327 Chirality : 0.043 0.169 3364 Planarity : 0.004 0.049 3854 Dihedral : 5.480 25.223 2992 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.50 % Favored : 91.46 % Rotamer: Outliers : 3.54 % Allowed : 16.79 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2706 helix: -0.97 (0.13), residues: 1516 sheet: -1.73 (0.46), residues: 130 loop : -1.66 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.047 0.001 PHE C 540 TYR 0.015 0.001 TYR D 210 ARG 0.007 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 898) hydrogen bonds : angle 4.11184 ( 2535) covalent geometry : bond 0.00385 (22552) covalent geometry : angle 0.64019 (30484) *********************** 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: 85 poor density : 234 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7633 (tmt170) cc_final: 0.5779 (ptt180) REVERT: A 193 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6867 (mtm-85) REVERT: A 206 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 320 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7472 (ttm110) REVERT: A 337 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8049 (tpp-160) REVERT: A 340 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7954 (mtp85) REVERT: A 430 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8163 (tm) REVERT: A 470 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7678 (mtp-110) REVERT: A 483 GLN cc_start: 0.8904 (tp40) cc_final: 0.8612 (tp40) REVERT: A 490 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 519 ASP cc_start: 0.8227 (t0) cc_final: 0.7842 (t70) REVERT: A 523 HIS cc_start: 0.7884 (t-170) cc_final: 0.7554 (t-170) REVERT: A 623 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: A 666 HIS cc_start: 0.5945 (t-90) cc_final: 0.5275 (m170) REVERT: B 37 TRP cc_start: 0.6075 (m100) cc_final: 0.5826 (m100) REVERT: B 63 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.6611 (tmm160) REVERT: B 121 ARG cc_start: 0.7710 (tpm170) cc_final: 0.7082 (tpp-160) REVERT: B 137 PHE cc_start: 0.7838 (m-80) cc_final: 0.7210 (m-10) REVERT: B 204 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 301 TYR cc_start: 0.8167 (t80) cc_final: 0.7595 (m-80) REVERT: B 317 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: B 360 MET cc_start: 0.9107 (ppp) cc_final: 0.8576 (ppp) REVERT: B 493 PHE cc_start: 0.8671 (p90) cc_final: 0.8387 (p90) REVERT: B 546 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8522 (tp-100) REVERT: B 642 ASP cc_start: 0.8735 (p0) cc_final: 0.8446 (p0) REVERT: B 666 HIS cc_start: 0.7368 (t70) cc_final: 0.6331 (t-170) REVERT: B 698 LEU cc_start: 0.9131 (tt) cc_final: 0.8895 (mp) REVERT: C 317 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 351 TYR cc_start: 0.8805 (t80) cc_final: 0.8597 (t80) REVERT: C 354 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6969 (p-80) REVERT: C 403 HIS cc_start: 0.7753 (m90) cc_final: 0.7365 (m-70) REVERT: C 405 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 479 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7135 (mtm-85) REVERT: C 504 MET cc_start: 0.7479 (tpp) cc_final: 0.7083 (mmt) REVERT: C 530 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: C 552 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8163 (mpt90) REVERT: C 574 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: C 615 LEU cc_start: 0.9013 (mt) cc_final: 0.8786 (mp) REVERT: C 618 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8864 (mmpt) REVERT: C 661 HIS cc_start: 0.8042 (m-70) cc_final: 0.6979 (m90) REVERT: D 51 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.6016 (t70) REVERT: D 70 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6573 (tmm) REVERT: D 369 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7861 (mtm180) REVERT: D 432 GLU cc_start: 0.8243 (tt0) cc_final: 0.7681 (tt0) REVERT: D 436 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7381 (t) REVERT: D 481 ASP cc_start: 0.7775 (p0) cc_final: 0.7407 (t0) REVERT: D 642 ASP cc_start: 0.8663 (m-30) cc_final: 0.8294 (m-30) REVERT: D 645 LYS cc_start: 0.9172 (tptp) cc_final: 0.8688 (mtmm) REVERT: D 661 HIS cc_start: 0.7962 (m90) cc_final: 0.7612 (m170) REVERT: D 666 HIS cc_start: 0.7155 (m-70) cc_final: 0.6362 (m-70) REVERT: D 671 GLU cc_start: 0.8780 (tp30) cc_final: 0.8219 (tp30) REVERT: D 673 LEU cc_start: 0.7976 (mt) cc_final: 0.7467 (mt) REVERT: D 702 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8038 (mtm180) outliers start: 85 outliers final: 27 residues processed: 295 average time/residue: 1.1728 time to fit residues: 401.7747 Evaluate side-chains 261 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 354 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 623 PHE 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 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 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 665 LEU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 309 LEU 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 590 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 713 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.0770 chunk 135 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099777 restraints weight = 31980.789| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.20 r_work: 0.3144 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22552 Z= 0.112 Angle : 0.620 17.735 30484 Z= 0.312 Chirality : 0.042 0.179 3364 Planarity : 0.004 0.048 3854 Dihedral : 5.181 25.036 2992 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 2.96 % Allowed : 17.92 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2706 helix: -0.64 (0.13), residues: 1502 sheet: -1.60 (0.46), residues: 130 loop : -1.56 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.018 0.001 PHE C 467 TYR 0.017 0.001 TYR C 492 ARG 0.008 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 898) hydrogen bonds : angle 3.90948 ( 2535) covalent geometry : bond 0.00246 (22552) covalent geometry : angle 0.61975 (30484) *********************** 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 316 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 2.470 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: 0.7592 (tmt170) cc_final: 0.5787 (ptt180) REVERT: A 193 ARG cc_start: 0.7038 (mtm180) cc_final: 0.6821 (mtm-85) REVERT: A 320 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7391 (ttm110) REVERT: A 337 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8014 (tpp-160) REVERT: A 408 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 430 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8157 (tm) REVERT: A 470 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7659 (mtp-110) REVERT: A 483 GLN cc_start: 0.8927 (tp40) cc_final: 0.8613 (tp40) REVERT: A 519 ASP cc_start: 0.8291 (t0) cc_final: 0.7846 (t70) REVERT: A 623 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: A 666 HIS cc_start: 0.5848 (t-90) cc_final: 0.5200 (m170) REVERT: A 676 MET cc_start: 0.8124 (tpp) cc_final: 0.7856 (tpp) REVERT: B 37 TRP cc_start: 0.5970 (m100) cc_final: 0.5739 (m100) REVERT: B 63 ARG cc_start: 0.7562 (tmm-80) cc_final: 0.6531 (tmm160) REVERT: B 121 ARG cc_start: 0.7533 (tpm170) cc_final: 0.6940 (tpp-160) REVERT: B 137 PHE cc_start: 0.7786 (m-80) cc_final: 0.7150 (m-10) REVERT: B 317 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: B 493 PHE cc_start: 0.8690 (p90) cc_final: 0.8374 (p90) REVERT: B 546 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8471 (tp-100) REVERT: B 552 ARG cc_start: 0.8294 (mmp80) cc_final: 0.7973 (mmp80) REVERT: B 642 ASP cc_start: 0.8719 (p0) cc_final: 0.8461 (p0) REVERT: B 652 MET cc_start: 0.8217 (mmm) cc_final: 0.7896 (tpt) REVERT: B 673 LEU cc_start: 0.7937 (mm) cc_final: 0.7607 (mp) REVERT: B 702 ARG cc_start: 0.8619 (ppt90) cc_final: 0.8378 (mtt-85) REVERT: C 210 TYR cc_start: 0.8396 (m-80) cc_final: 0.8093 (m-80) REVERT: C 351 TYR cc_start: 0.8738 (t80) cc_final: 0.8527 (t80) REVERT: C 354 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: C 403 HIS cc_start: 0.7748 (m90) cc_final: 0.7371 (m-70) REVERT: C 405 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 479 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6914 (mtm-85) REVERT: C 530 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: C 552 ARG cc_start: 0.8940 (mtt90) cc_final: 0.8623 (mmt-90) REVERT: C 615 LEU cc_start: 0.9001 (mt) cc_final: 0.8746 (mp) REVERT: C 618 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8851 (mmpt) REVERT: C 661 HIS cc_start: 0.7993 (m-70) cc_final: 0.6876 (m90) REVERT: C 676 MET cc_start: 0.8287 (mmt) cc_final: 0.8058 (mmt) REVERT: D 64 TRP cc_start: 0.8456 (m100) cc_final: 0.7669 (m-10) REVERT: D 70 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6420 (tmt) REVERT: D 369 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7762 (mtm180) REVERT: D 432 GLU cc_start: 0.8222 (tt0) cc_final: 0.7692 (tt0) REVERT: D 481 ASP cc_start: 0.7710 (p0) cc_final: 0.7445 (t0) REVERT: D 501 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8477 (p0) REVERT: D 524 ILE cc_start: 0.3559 (OUTLIER) cc_final: 0.3334 (mp) REVERT: D 661 HIS cc_start: 0.7966 (m90) cc_final: 0.7614 (m170) REVERT: D 666 HIS cc_start: 0.6978 (m-70) cc_final: 0.6195 (m-70) REVERT: D 673 LEU cc_start: 0.7799 (mt) cc_final: 0.7587 (mt) REVERT: D 702 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8002 (mtm-85) outliers start: 71 outliers final: 18 residues processed: 294 average time/residue: 1.1859 time to fit residues: 408.0469 Evaluate side-chains 238 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR 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 641 SER Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 354 HIS 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 501 ASN Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 148 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.152009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092576 restraints weight = 31977.708| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.38 r_work: 0.3038 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3016 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= 0.242 Angle : 0.705 18.649 30484 Z= 0.355 Chirality : 0.046 0.179 3364 Planarity : 0.004 0.054 3854 Dihedral : 5.384 25.884 2992 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.28 % Favored : 90.69 % Rotamer: Outliers : 3.29 % Allowed : 18.25 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2706 helix: -0.75 (0.13), residues: 1521 sheet: -1.66 (0.46), residues: 130 loop : -1.48 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.019 0.002 PHE A 287 TYR 0.015 0.002 TYR C 258 ARG 0.009 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 898) hydrogen bonds : angle 4.16630 ( 2535) covalent geometry : bond 0.00578 (22552) covalent geometry : angle 0.70545 (30484) *********************** 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 306 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7652 (tmt170) cc_final: 0.5786 (ptt180) REVERT: A 193 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6951 (mtm-85) REVERT: A 206 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 320 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7528 (ttm110) REVERT: A 337 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.7948 (tpp-160) REVERT: A 470 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7746 (mtp-110) REVERT: A 483 GLN cc_start: 0.8996 (tp40) cc_final: 0.8734 (tp40) REVERT: A 519 ASP cc_start: 0.8492 (t0) cc_final: 0.8096 (t70) REVERT: A 623 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 37 TRP cc_start: 0.6157 (m100) cc_final: 0.5891 (m100) REVERT: B 63 ARG cc_start: 0.7630 (tmm-80) cc_final: 0.6623 (tmm160) REVERT: B 121 ARG cc_start: 0.7730 (tpm170) cc_final: 0.6892 (tpp-160) REVERT: B 137 PHE cc_start: 0.7888 (m-80) cc_final: 0.7263 (m-10) REVERT: B 204 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8088 (mm) REVERT: B 301 TYR cc_start: 0.8246 (t80) cc_final: 0.7659 (m-80) REVERT: B 317 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 360 MET cc_start: 0.9068 (ppp) cc_final: 0.8563 (ppp) REVERT: B 493 PHE cc_start: 0.8706 (p90) cc_final: 0.8424 (p90) REVERT: B 550 LEU cc_start: 0.9126 (mt) cc_final: 0.8916 (mt) REVERT: B 552 ARG cc_start: 0.8394 (mmp80) cc_final: 0.8143 (mmp80) REVERT: B 588 VAL cc_start: 0.5539 (OUTLIER) cc_final: 0.5279 (m) REVERT: B 642 ASP cc_start: 0.8743 (p0) cc_final: 0.8401 (p0) REVERT: B 652 MET cc_start: 0.8333 (mmm) cc_final: 0.7865 (tpt) REVERT: B 673 LEU cc_start: 0.8018 (mm) cc_final: 0.7613 (mp) REVERT: B 699 ASP cc_start: 0.8320 (p0) cc_final: 0.8114 (p0) REVERT: C 403 HIS cc_start: 0.7862 (m90) cc_final: 0.7455 (m-70) REVERT: C 405 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 479 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7351 (mtm-85) REVERT: C 530 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: C 552 ARG cc_start: 0.8916 (mtt90) cc_final: 0.8625 (mmt-90) REVERT: C 615 LEU cc_start: 0.9013 (mt) cc_final: 0.8718 (mp) REVERT: C 618 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8890 (mmpt) REVERT: C 661 HIS cc_start: 0.8032 (m-70) cc_final: 0.6976 (m90) REVERT: D 70 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6950 (tmt) REVERT: D 337 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7686 (ptm-80) REVERT: D 369 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7867 (mtm180) REVERT: D 432 GLU cc_start: 0.8281 (tt0) cc_final: 0.7812 (tt0) REVERT: D 481 ASP cc_start: 0.7835 (p0) cc_final: 0.7461 (t0) REVERT: D 493 PHE cc_start: 0.8176 (p90) cc_final: 0.7700 (p90) REVERT: D 524 ILE cc_start: 0.3740 (OUTLIER) cc_final: 0.3456 (mp) REVERT: D 642 ASP cc_start: 0.8703 (m-30) cc_final: 0.8363 (m-30) REVERT: D 645 LYS cc_start: 0.9174 (tptp) cc_final: 0.8560 (mtmp) REVERT: D 666 HIS cc_start: 0.7096 (m-70) cc_final: 0.6311 (m-70) REVERT: D 671 GLU cc_start: 0.8813 (tp30) cc_final: 0.8198 (tp30) REVERT: D 673 LEU cc_start: 0.7917 (mt) cc_final: 0.7364 (mt) REVERT: D 702 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7967 (mtm-85) outliers start: 79 outliers final: 33 residues processed: 281 average time/residue: 1.1021 time to fit residues: 363.3727 Evaluate side-chains 254 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 2.589 ------------------------------------------------------------------------------- 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 363 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain 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 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 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 33 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 258 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 225 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 585 GLN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN D 609 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098756 restraints weight = 31833.788| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.14 r_work: 0.3155 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22552 Z= 0.120 Angle : 0.651 18.688 30484 Z= 0.322 Chirality : 0.042 0.179 3364 Planarity : 0.004 0.056 3854 Dihedral : 5.124 25.107 2992 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.98 % Favored : 91.98 % Rotamer: Outliers : 2.54 % Allowed : 19.96 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2706 helix: -0.55 (0.13), residues: 1527 sheet: -1.54 (0.46), residues: 130 loop : -1.44 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 255 HIS 0.010 0.001 HIS D 494 PHE 0.019 0.001 PHE D 544 TYR 0.022 0.001 TYR D 355 ARG 0.010 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 898) hydrogen bonds : angle 3.89824 ( 2535) covalent geometry : bond 0.00272 (22552) covalent geometry : angle 0.65146 (30484) *********************** 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 286 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7593 (tmt170) cc_final: 0.5741 (ptt180) REVERT: A 193 ARG cc_start: 0.7107 (mtm180) cc_final: 0.6868 (mtm-85) REVERT: A 320 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7463 (ttm110) REVERT: A 337 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.7936 (tpp-160) REVERT: A 470 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7701 (mtp-110) REVERT: A 483 GLN cc_start: 0.8897 (tp40) cc_final: 0.8556 (tp40) REVERT: A 519 ASP cc_start: 0.8459 (t0) cc_final: 0.8160 (t70) REVERT: A 623 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: A 666 HIS cc_start: 0.5895 (t-90) cc_final: 0.5316 (m170) REVERT: B 37 TRP cc_start: 0.5839 (m100) cc_final: 0.5605 (m100) REVERT: B 63 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.6603 (tmm160) REVERT: B 121 ARG cc_start: 0.7435 (tpm170) cc_final: 0.6877 (tpp-160) REVERT: B 137 PHE cc_start: 0.7770 (m-80) cc_final: 0.7142 (m-10) REVERT: B 317 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: B 330 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8434 (mtm) REVERT: B 360 MET cc_start: 0.9086 (ppp) cc_final: 0.8573 (ppp) REVERT: B 362 GLN cc_start: 0.8980 (pm20) cc_final: 0.8768 (pm20) REVERT: B 552 ARG cc_start: 0.8325 (mmp80) cc_final: 0.8045 (mmp80) REVERT: B 642 ASP cc_start: 0.8685 (p0) cc_final: 0.8390 (p0) REVERT: B 652 MET cc_start: 0.8340 (mmm) cc_final: 0.7829 (tpt) REVERT: B 673 LEU cc_start: 0.7950 (mm) cc_final: 0.7620 (mp) REVERT: B 702 ARG cc_start: 0.8573 (ppt90) cc_final: 0.8291 (mtt-85) REVERT: C 210 TYR cc_start: 0.8361 (m-80) cc_final: 0.8061 (m-80) REVERT: C 319 PHE cc_start: 0.8615 (t80) cc_final: 0.8373 (t80) REVERT: C 323 MET cc_start: 0.8367 (ttp) cc_final: 0.8067 (mtm) REVERT: C 403 HIS cc_start: 0.7748 (m90) cc_final: 0.7371 (m-70) REVERT: C 405 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7577 (mt-10) REVERT: C 479 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7117 (mtm-85) REVERT: C 530 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: C 552 ARG cc_start: 0.8912 (mtt90) cc_final: 0.8625 (mmt-90) REVERT: C 615 LEU cc_start: 0.9002 (mt) cc_final: 0.8800 (mp) REVERT: D 64 TRP cc_start: 0.8453 (m100) cc_final: 0.7722 (m-10) REVERT: D 70 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6633 (tmt) REVERT: D 369 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7884 (mtm180) REVERT: D 432 GLU cc_start: 0.8209 (tt0) cc_final: 0.7736 (tt0) REVERT: D 481 ASP cc_start: 0.7767 (p0) cc_final: 0.7544 (t0) REVERT: D 524 ILE cc_start: 0.3332 (OUTLIER) cc_final: 0.3054 (mp) REVERT: D 645 LYS cc_start: 0.9037 (tptp) cc_final: 0.8555 (mtmm) REVERT: D 666 HIS cc_start: 0.7012 (m-70) cc_final: 0.6220 (m-70) REVERT: D 673 LEU cc_start: 0.7793 (mt) cc_final: 0.7585 (mt) REVERT: D 702 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7937 (mtm-85) outliers start: 61 outliers final: 20 residues processed: 269 average time/residue: 1.1410 time to fit residues: 359.0465 Evaluate side-chains 234 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 316 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 209 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 674 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 211 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 216 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 112 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 251 optimal weight: 0.7980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4093 r_free = 0.4093 target = 0.156611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098360 restraints weight = 31789.103| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22552 Z= 0.125 Angle : 0.655 18.379 30484 Z= 0.324 Chirality : 0.043 0.201 3364 Planarity : 0.004 0.056 3854 Dihedral : 5.038 25.796 2992 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 2.29 % Allowed : 20.46 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2706 helix: -0.44 (0.13), residues: 1536 sheet: -1.51 (0.46), residues: 130 loop : -1.33 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.018 0.001 PHE C 467 TYR 0.018 0.001 TYR C 351 ARG 0.010 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 898) hydrogen bonds : angle 3.87923 ( 2535) covalent geometry : bond 0.00284 (22552) covalent geometry : angle 0.65509 (30484) *********************** 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 273 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7562 (tmt170) cc_final: 0.5779 (ptt180) REVERT: A 193 ARG cc_start: 0.7097 (mtm180) cc_final: 0.6858 (mtm-85) REVERT: A 320 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7514 (ttm110) REVERT: A 337 ARG cc_start: 0.8515 (tpp-160) cc_final: 0.7901 (tpp-160) REVERT: A 430 LEU cc_start: 0.8299 (tm) cc_final: 0.7967 (tm) REVERT: A 470 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7648 (mtp-110) REVERT: A 483 GLN cc_start: 0.8900 (tp40) cc_final: 0.8523 (tp40) REVERT: A 519 ASP cc_start: 0.8490 (t0) cc_final: 0.8145 (t0) REVERT: A 623 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 666 HIS cc_start: 0.5995 (t-90) cc_final: 0.5391 (m170) REVERT: B 37 TRP cc_start: 0.5857 (m100) cc_final: 0.5627 (m100) REVERT: B 63 ARG cc_start: 0.7547 (tmm-80) cc_final: 0.6523 (tmm160) REVERT: B 121 ARG cc_start: 0.7496 (tpm170) cc_final: 0.6874 (tpp-160) REVERT: B 137 PHE cc_start: 0.7766 (m-80) cc_final: 0.7158 (m-10) REVERT: B 204 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 317 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: B 360 MET cc_start: 0.9090 (ppp) cc_final: 0.8615 (ppp) REVERT: B 362 GLN cc_start: 0.8992 (pm20) cc_final: 0.8784 (pm20) REVERT: B 550 LEU cc_start: 0.8965 (mt) cc_final: 0.8703 (mp) REVERT: B 552 ARG cc_start: 0.8384 (mmp80) cc_final: 0.8094 (mmp80) REVERT: B 642 ASP cc_start: 0.8746 (p0) cc_final: 0.8456 (p0) REVERT: B 673 LEU cc_start: 0.7999 (mm) cc_final: 0.7705 (mp) REVERT: B 675 LEU cc_start: 0.8356 (tm) cc_final: 0.8146 (pp) REVERT: B 702 ARG cc_start: 0.8545 (ppt90) cc_final: 0.8272 (mtt-85) REVERT: C 194 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 210 TYR cc_start: 0.8416 (m-80) cc_final: 0.8188 (m-80) REVERT: C 319 PHE cc_start: 0.8568 (t80) cc_final: 0.8334 (t80) REVERT: C 323 MET cc_start: 0.8321 (ttp) cc_final: 0.7999 (mtm) REVERT: C 403 HIS cc_start: 0.7735 (m90) cc_final: 0.7336 (m-70) REVERT: C 405 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 479 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7066 (mtm-85) REVERT: C 530 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: C 552 ARG cc_start: 0.8932 (mtt90) cc_final: 0.8621 (mmt-90) REVERT: C 615 LEU cc_start: 0.9017 (mt) cc_final: 0.8777 (mp) REVERT: C 661 HIS cc_start: 0.7963 (m-70) cc_final: 0.6848 (m-70) REVERT: D 64 TRP cc_start: 0.8471 (m100) cc_final: 0.7765 (m-10) REVERT: D 70 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6602 (tmt) REVERT: D 369 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7816 (mtm180) REVERT: D 398 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7782 (tt) REVERT: D 432 GLU cc_start: 0.8255 (tt0) cc_final: 0.7726 (tt0) REVERT: D 481 ASP cc_start: 0.7725 (p0) cc_final: 0.7485 (t0) REVERT: D 524 ILE cc_start: 0.3709 (OUTLIER) cc_final: 0.3270 (mp) REVERT: D 543 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7656 (p0) REVERT: D 645 LYS cc_start: 0.9169 (tptp) cc_final: 0.8554 (mtmm) REVERT: D 666 HIS cc_start: 0.6990 (m-70) cc_final: 0.6167 (m-70) REVERT: D 671 GLU cc_start: 0.8787 (tp30) cc_final: 0.8144 (tp30) REVERT: D 673 LEU cc_start: 0.7602 (mt) cc_final: 0.6929 (mt) outliers start: 55 outliers final: 20 residues processed: 255 average time/residue: 1.1932 time to fit residues: 354.5763 Evaluate side-chains 238 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain 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 583 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 363 ASP 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 524 ILE Chi-restraints excluded: chain D residue 543 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 113 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 210 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 422 HIS ** 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 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.156727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099134 restraints weight = 31896.629| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3137 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3337 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= 0.130 Angle : 0.673 19.407 30484 Z= 0.330 Chirality : 0.043 0.297 3364 Planarity : 0.004 0.067 3854 Dihedral : 5.005 25.302 2992 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.28 % Favored : 91.69 % Rotamer: Outliers : 2.00 % Allowed : 20.67 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2706 helix: -0.37 (0.14), residues: 1537 sheet: -1.49 (0.46), residues: 132 loop : -1.27 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.020 0.001 PHE C 467 TYR 0.024 0.001 TYR B 120 ARG 0.018 0.000 ARG D 702 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 898) hydrogen bonds : angle 3.88584 ( 2535) covalent geometry : bond 0.00298 (22552) covalent geometry : angle 0.67310 (30484) *********************** 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 269 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7550 (tmt170) cc_final: 0.5804 (ptt180) REVERT: A 193 ARG cc_start: 0.7062 (mtm180) cc_final: 0.6820 (mtm-85) REVERT: A 320 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7543 (ttm110) REVERT: A 337 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.7924 (tpp-160) REVERT: A 430 LEU cc_start: 0.8312 (tm) cc_final: 0.7969 (tm) REVERT: A 470 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7727 (mtp-110) REVERT: A 483 GLN cc_start: 0.8896 (tp40) cc_final: 0.8523 (tp40) REVERT: A 519 ASP cc_start: 0.8522 (t0) cc_final: 0.8167 (t0) REVERT: A 623 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: A 679 MET cc_start: 0.7941 (pmm) cc_final: 0.7492 (pmm) REVERT: B 37 TRP cc_start: 0.5877 (m100) cc_final: 0.5662 (m100) REVERT: B 63 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.6586 (tmm160) REVERT: B 121 ARG cc_start: 0.7515 (tpm170) cc_final: 0.6894 (tpp-160) REVERT: B 137 PHE cc_start: 0.7797 (m-80) cc_final: 0.7203 (m-10) REVERT: B 204 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8120 (mm) REVERT: B 317 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: B 330 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8574 (mtm) REVERT: B 360 MET cc_start: 0.9123 (ppp) cc_final: 0.8626 (ppp) REVERT: B 362 GLN cc_start: 0.9003 (pm20) cc_final: 0.8798 (pm20) REVERT: B 550 LEU cc_start: 0.9030 (mt) cc_final: 0.8793 (mp) REVERT: B 552 ARG cc_start: 0.8390 (mmp80) cc_final: 0.8129 (mmp80) REVERT: B 642 ASP cc_start: 0.8745 (p0) cc_final: 0.8457 (p0) REVERT: B 652 MET cc_start: 0.8291 (mmm) cc_final: 0.8088 (tpt) REVERT: B 673 LEU cc_start: 0.8161 (mm) cc_final: 0.7909 (mp) REVERT: B 702 ARG cc_start: 0.8530 (ppt90) cc_final: 0.8230 (mtt-85) REVERT: C 210 TYR cc_start: 0.8364 (m-80) cc_final: 0.8143 (m-80) REVERT: C 319 PHE cc_start: 0.8621 (t80) cc_final: 0.8299 (t80) REVERT: C 323 MET cc_start: 0.8375 (ttp) cc_final: 0.8085 (mtm) REVERT: C 403 HIS cc_start: 0.7764 (m90) cc_final: 0.7401 (m-70) REVERT: C 405 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 479 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: C 530 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: C 552 ARG cc_start: 0.8890 (mtt90) cc_final: 0.8613 (mmt-90) REVERT: C 615 LEU cc_start: 0.9018 (mt) cc_final: 0.8775 (mp) REVERT: C 661 HIS cc_start: 0.8027 (m-70) cc_final: 0.6908 (m-70) REVERT: D 64 TRP cc_start: 0.8454 (m100) cc_final: 0.7792 (m-10) REVERT: D 70 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6678 (tmt) REVERT: D 126 TYR cc_start: 0.7321 (m-10) cc_final: 0.7086 (m-10) REVERT: D 369 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7833 (mtm180) REVERT: D 432 GLU cc_start: 0.8246 (tt0) cc_final: 0.7769 (tt0) REVERT: D 481 ASP cc_start: 0.7733 (p0) cc_final: 0.7528 (t0) REVERT: D 524 ILE cc_start: 0.3647 (OUTLIER) cc_final: 0.3313 (mp) REVERT: D 543 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7659 (p0) REVERT: D 645 LYS cc_start: 0.9136 (tptp) cc_final: 0.8560 (mtmm) REVERT: D 666 HIS cc_start: 0.7058 (m-70) cc_final: 0.6232 (m-70) REVERT: D 671 GLU cc_start: 0.8765 (tp30) cc_final: 0.8143 (tp30) REVERT: D 673 LEU cc_start: 0.7597 (mt) cc_final: 0.6917 (mt) REVERT: D 702 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7723 (mtm-85) outliers start: 48 outliers final: 22 residues processed: 253 average time/residue: 1.2069 time to fit residues: 356.7017 Evaluate side-chains 241 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain 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 330 MET 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 605 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 382 LYS 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 520 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 543 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 242 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 422 HIS ** 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 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097031 restraints weight = 31846.890| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.25 r_work: 0.3108 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22552 Z= 0.149 Angle : 0.679 19.258 30484 Z= 0.333 Chirality : 0.044 0.215 3364 Planarity : 0.004 0.084 3854 Dihedral : 5.022 25.496 2992 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.43 % Favored : 91.54 % Rotamer: Outliers : 1.75 % Allowed : 21.12 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2706 helix: -0.33 (0.14), residues: 1531 sheet: -1.50 (0.46), residues: 132 loop : -1.28 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.021 0.001 PHE D 623 TYR 0.017 0.001 TYR C 492 ARG 0.019 0.000 ARG D 702 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 898) hydrogen bonds : angle 3.93624 ( 2535) covalent geometry : bond 0.00350 (22552) covalent geometry : angle 0.67855 (30484) ********************** 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 271 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7553 (tmt170) cc_final: 0.5770 (ptt180) REVERT: A 193 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6888 (mtm-85) REVERT: A 320 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7474 (ttm110) REVERT: A 337 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.7892 (tpp-160) REVERT: A 430 LEU cc_start: 0.8261 (tm) cc_final: 0.7882 (tm) REVERT: A 470 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7670 (mtp-110) REVERT: A 483 GLN cc_start: 0.8916 (tp40) cc_final: 0.8519 (tp40) REVERT: A 519 ASP cc_start: 0.8519 (t0) cc_final: 0.8197 (t0) REVERT: A 623 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 679 MET cc_start: 0.8053 (pmm) cc_final: 0.7647 (pmm) REVERT: B 37 TRP cc_start: 0.5854 (m100) cc_final: 0.5615 (m100) REVERT: B 63 ARG cc_start: 0.7564 (tmm-80) cc_final: 0.6529 (tmm160) REVERT: B 121 ARG cc_start: 0.7615 (tpm170) cc_final: 0.7207 (tpt170) REVERT: B 137 PHE cc_start: 0.7806 (m-80) cc_final: 0.7210 (m-10) REVERT: B 204 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8084 (mm) REVERT: B 301 TYR cc_start: 0.8088 (t80) cc_final: 0.7598 (m-80) REVERT: B 317 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: B 360 MET cc_start: 0.9104 (ppp) cc_final: 0.8649 (ppp) REVERT: B 362 GLN cc_start: 0.9024 (pm20) cc_final: 0.8809 (pm20) REVERT: B 493 PHE cc_start: 0.8655 (p90) cc_final: 0.8429 (p90) REVERT: B 550 LEU cc_start: 0.8996 (mt) cc_final: 0.8745 (mp) REVERT: B 552 ARG cc_start: 0.8417 (mmp80) cc_final: 0.8045 (mmp80) REVERT: B 642 ASP cc_start: 0.8772 (p0) cc_final: 0.8495 (p0) REVERT: B 652 MET cc_start: 0.8312 (mmm) cc_final: 0.7988 (tpt) REVERT: B 673 LEU cc_start: 0.8034 (mm) cc_final: 0.7718 (mp) REVERT: B 702 ARG cc_start: 0.8609 (ppt90) cc_final: 0.8255 (mtt-85) REVERT: C 319 PHE cc_start: 0.8613 (t80) cc_final: 0.8321 (t80) REVERT: C 323 MET cc_start: 0.8383 (ttp) cc_final: 0.8106 (mtm) REVERT: C 403 HIS cc_start: 0.7785 (m90) cc_final: 0.7393 (m-70) REVERT: C 405 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 479 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7201 (mtm-85) REVERT: C 530 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: C 552 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8619 (mmt-90) REVERT: C 615 LEU cc_start: 0.8989 (mt) cc_final: 0.8739 (mp) REVERT: C 661 HIS cc_start: 0.7950 (m-70) cc_final: 0.6832 (m-70) REVERT: D 64 TRP cc_start: 0.8461 (m100) cc_final: 0.7782 (m-10) REVERT: D 70 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6704 (tmt) REVERT: D 126 TYR cc_start: 0.7439 (m-10) cc_final: 0.7222 (m-10) REVERT: D 363 ASP cc_start: 0.8698 (p0) cc_final: 0.8491 (p0) REVERT: D 369 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7789 (mtm180) REVERT: D 398 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7708 (tt) REVERT: D 432 GLU cc_start: 0.8250 (tt0) cc_final: 0.7722 (tt0) REVERT: D 481 ASP cc_start: 0.7699 (p0) cc_final: 0.7434 (t0) REVERT: D 524 ILE cc_start: 0.3899 (OUTLIER) cc_final: 0.3566 (mp) REVERT: D 543 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7715 (p0) REVERT: D 666 HIS cc_start: 0.6942 (m-70) cc_final: 0.6158 (m-70) REVERT: D 671 GLU cc_start: 0.8835 (tp30) cc_final: 0.8206 (tp30) REVERT: D 673 LEU cc_start: 0.7603 (mt) cc_final: 0.6974 (mt) REVERT: D 702 ARG cc_start: 0.8356 (ttm110) cc_final: 0.7856 (mtm-85) outliers start: 42 outliers final: 27 residues processed: 258 average time/residue: 1.1567 time to fit residues: 347.5457 Evaluate side-chains 251 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 85 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 330 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 428 GLU 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 520 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 715 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 227 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 422 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.156517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097853 restraints weight = 31832.714| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.24 r_work: 0.3130 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22552 Z= 0.129 Angle : 0.682 19.242 30484 Z= 0.336 Chirality : 0.043 0.196 3364 Planarity : 0.004 0.077 3854 Dihedral : 4.966 25.354 2992 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 1.79 % Allowed : 21.38 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2706 helix: -0.30 (0.14), residues: 1540 sheet: -1.44 (0.46), residues: 132 loop : -1.19 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS D 43 PHE 0.023 0.001 PHE C 467 TYR 0.021 0.001 TYR C 492 ARG 0.018 0.000 ARG D 702 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 898) hydrogen bonds : angle 3.92015 ( 2535) covalent geometry : bond 0.00297 (22552) covalent geometry : angle 0.68247 (30484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20737.07 seconds wall clock time: 358 minutes 56.98 seconds (21536.98 seconds total)