Starting phenix.real_space_refine on Fri Mar 6 02:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8w_15242/03_2026/8a8w_15242.map" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.118 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 P 20 5.49 5 S 66 5.16 5 C 17060 2.51 5 N 4842 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27187 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4537 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4370 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 531} Chain breaks: 5 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.31, per 1000 atoms: 0.23 Number of scatterers: 27187 At special positions: 0 Unit cell: (123.12, 140.22, 152.19, 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) S 66 16.00 P 20 15.00 O 5199 8.00 N 4842 7.00 C 17060 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 29 sheets defined 59.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.580A pdb=" N HIS A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.668A pdb=" N LYS A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.435A pdb=" N GLY A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 351 through 371 removed outlier: 5.182A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.621A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 415 Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.876A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.755A pdb=" N LEU A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.513A pdb=" N ALA A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.550A pdb=" N ALA A 576 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 577' Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.899A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 690 through 705 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 743 Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 772 through 791 removed outlier: 3.966A pdb=" N GLN A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP A 783 " --> pdb=" O ARG A 779 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLN A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.736A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.559A pdb=" N VAL B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 251 through 258 removed outlier: 4.470A pdb=" N GLY B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.655A pdb=" N VAL B 293 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.648A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 351 through 371 removed outlier: 4.519A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 396 through 415 Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 500 through 516 removed outlier: 5.222A pdb=" N GLU B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.509A pdb=" N GLY B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 removed outlier: 3.540A pdb=" N LYS B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.707A pdb=" N LYS B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.899A pdb=" N LYS B 629 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 626 through 630' Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.753A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.632A pdb=" N ARG B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.852A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 781 through 791 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.675A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 174' Processing helix chain 'C' and resid 178 through 185 removed outlier: 3.714A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.774A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.828A pdb=" N LYS C 243 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 280 removed outlier: 3.756A pdb=" N PHE C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.719A pdb=" N GLU C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 371 removed outlier: 5.050A pdb=" N ASP C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.610A pdb=" N MET C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 415 removed outlier: 3.647A pdb=" N MET C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 493 removed outlier: 3.612A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 518 removed outlier: 3.695A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.590A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 594 removed outlier: 3.672A pdb=" N ALA C 591 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 617 Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 644 removed outlier: 3.943A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 723 through 743 Processing helix chain 'C' and resid 744 through 746 No H-bonds generated for 'chain 'C' and resid 744 through 746' Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 773 through 781 Processing helix chain 'C' and resid 781 through 791 removed outlier: 3.606A pdb=" N PHE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.595A pdb=" N GLY D 175 " --> pdb=" O ASP D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 removed outlier: 4.194A pdb=" N GLU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.768A pdb=" N ILE D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 236 removed outlier: 4.533A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 removed outlier: 3.862A pdb=" N LEU D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 288 through 292 removed outlier: 3.909A pdb=" N THR D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.818A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Proline residue: D 310 - end of helix removed outlier: 3.573A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 removed outlier: 3.807A pdb=" N ILE D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.572A pdb=" N GLU D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 370 removed outlier: 4.591A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.987A pdb=" N MET D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 415 Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 509 through 516 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 558 through 572 removed outlier: 3.880A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 585 No H-bonds generated for 'chain 'D' and resid 583 through 585' Processing helix chain 'D' and resid 587 through 590 removed outlier: 3.530A pdb=" N THR D 590 " --> pdb=" O ASP D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 587 through 590' Processing helix chain 'D' and resid 591 through 596 removed outlier: 4.191A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 634 through 642 removed outlier: 4.157A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 705 Processing helix chain 'D' and resid 706 through 711 Processing helix chain 'D' and resid 723 through 744 removed outlier: 3.937A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.853A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 263 through 280 Processing helix chain 'E' and resid 288 through 292 Processing helix chain 'E' and resid 303 through 314 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.505A pdb=" N TYR E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.948A pdb=" N GLU E 339 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 340' Processing helix chain 'E' and resid 351 through 362 Processing helix chain 'E' and resid 362 through 371 removed outlier: 4.018A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.716A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 415 Processing helix chain 'E' and resid 480 through 493 removed outlier: 3.591A pdb=" N ILE E 484 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 Processing helix chain 'E' and resid 509 through 516 removed outlier: 3.805A pdb=" N GLU E 513 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 558 through 572 removed outlier: 3.868A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 585 No H-bonds generated for 'chain 'E' and resid 583 through 585' Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.738A pdb=" N PHE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 617 Processing helix chain 'E' and resid 626 through 630 removed outlier: 3.602A pdb=" N ALA E 630 " --> pdb=" O ILE E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 645 removed outlier: 4.066A pdb=" N TYR E 635 " --> pdb=" O HIS E 631 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 705 Processing helix chain 'E' and resid 706 through 712 Processing helix chain 'E' and resid 723 through 743 removed outlier: 3.795A pdb=" N ARG E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 738 " --> pdb=" O MET E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 746 No H-bonds generated for 'chain 'E' and resid 744 through 746' Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 770 through 781 Processing helix chain 'E' and resid 781 through 791 removed outlier: 3.619A pdb=" N LEU E 785 " --> pdb=" O ILE E 781 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 removed outlier: 4.067A pdb=" N GLU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 221 through 236 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 264 through 280 Processing helix chain 'F' and resid 289 through 292 Processing helix chain 'F' and resid 304 through 314 removed outlier: 3.739A pdb=" N LYS F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 324 through 331 Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.590A pdb=" N GLU F 339 " --> pdb=" O ASP F 335 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 340' Processing helix chain 'F' and resid 351 through 371 removed outlier: 4.341A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 Processing helix chain 'F' and resid 396 through 416 Processing helix chain 'F' and resid 480 through 493 Processing helix chain 'F' and resid 502 through 509 removed outlier: 3.697A pdb=" N ARG F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 516 removed outlier: 3.819A pdb=" N GLU F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.898A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 616 Processing helix chain 'F' and resid 627 through 630 Processing helix chain 'F' and resid 631 through 645 Processing helix chain 'F' and resid 688 through 704 Processing helix chain 'F' and resid 706 through 712 removed outlier: 3.691A pdb=" N LEU F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG F 712 " --> pdb=" O GLU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 744 removed outlier: 4.285A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 770 through 792 removed outlier: 4.097A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP F 783 " --> pdb=" O ARG F 779 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 784 " --> pdb=" O GLU F 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 251 removed outlier: 6.623A pdb=" N GLN A 246 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A 285 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 248 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP A 287 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 250 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 282 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 7.099A pdb=" N SER A 373 " --> pdb=" O VAL A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 581 removed outlier: 6.491A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 580 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 666 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE A 551 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE A 550 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 4.354A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 322 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 374 removed outlier: 6.356A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 578 through 581 removed outlier: 5.805A pdb=" N VAL B 622 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 665 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 624 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLY B 547 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 664 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 549 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 550 " --> pdb=" O ILE B 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.374A pdb=" N ALA B 748 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL B 802 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 750 " --> pdb=" O VAL B 802 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL B 804 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 817 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.275A pdb=" N GLN C 246 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE C 285 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR C 248 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP C 287 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 250 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 213 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 347 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 215 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.878A pdb=" N SER C 373 " --> pdb=" O VAL C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 578 through 581 removed outlier: 3.582A pdb=" N ASP C 715 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 Processing sheet with id=AB6, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.381A pdb=" N ALA C 748 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL C 802 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 750 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N VAL C 804 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 176 through 177 removed outlier: 6.122A pdb=" N GLN D 246 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 285 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR D 248 " --> pdb=" O PHE D 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 578 through 581 removed outlier: 6.741A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER D 548 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE D 717 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE D 550 " --> pdb=" O ILE D 717 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'D' and resid 748 through 751 removed outlier: 6.268A pdb=" N ALA D 748 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL D 802 " --> pdb=" O ALA D 748 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 750 " --> pdb=" O VAL D 802 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N VAL D 804 " --> pdb=" O VAL D 750 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.466A pdb=" N GLN E 246 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE E 285 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR E 248 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N ILE E 320 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU E 284 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ALA E 322 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 323 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.728A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.441A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER E 620 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE E 663 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 622 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR E 665 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE E 624 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY E 547 " --> pdb=" O LEU E 662 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE E 664 " --> pdb=" O GLY E 547 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE E 549 " --> pdb=" O PHE E 664 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER E 666 " --> pdb=" O PHE E 549 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE E 551 " --> pdb=" O SER E 666 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER E 548 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 717 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE E 550 " --> pdb=" O ILE E 717 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 646 through 648 Processing sheet with id=AC6, first strand: chain 'E' and resid 749 through 751 Processing sheet with id=AC7, first strand: chain 'F' and resid 175 through 177 removed outlier: 5.943A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP F 287 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU F 250 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 282 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE F 286 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR F 323 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU F 214 " --> pdb=" O THR F 323 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL F 345 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL F 213 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 373 through 374 removed outlier: 7.299A pdb=" N SER F 373 " --> pdb=" O VAL F 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 622 through 625 removed outlier: 6.310A pdb=" N VAL F 622 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR F 665 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE F 624 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY F 547 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE F 664 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE F 549 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER F 666 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE F 551 " --> pdb=" O SER F 666 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP F 715 " --> pdb=" O SER F 548 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 749 through 750 Processing sheet with id=AD2, first strand: chain 'F' and resid 803 through 805 removed outlier: 3.577A pdb=" N ASP F 805 " --> pdb=" O VAL F 817 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 817 " --> pdb=" O ASP F 805 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3840 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: 5.43 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8746 1.34 - 1.46: 3830 1.46 - 1.58: 14840 1.58 - 1.70: 30 1.70 - 1.82: 132 Bond restraints: 27578 Sorted by residual: bond pdb=" N LYS C 330 " pdb=" CA LYS C 330 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.89e+00 bond pdb=" CA ASP D 335 " pdb=" CB ASP D 335 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.70e-02 3.46e+03 4.78e+00 bond pdb=" N THR F 416 " pdb=" CA THR F 416 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.23e-02 6.61e+03 4.56e+00 bond pdb=" C LYS C 330 " pdb=" N TYR C 331 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.40e-02 5.10e+03 4.29e+00 bond pdb=" CA LYS C 330 " pdb=" C LYS C 330 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.34e-02 5.57e+03 3.44e+00 ... (remaining 27573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36411 2.49 - 4.97: 662 4.97 - 7.46: 116 7.46 - 9.95: 17 9.95 - 12.43: 1 Bond angle restraints: 37207 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" C LYS C 330 " pdb=" N TYR C 331 " pdb=" CA TYR C 331 " ideal model delta sigma weight residual 121.54 112.64 8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C LYS C 330 " pdb=" CA LYS C 330 " pdb=" CB LYS C 330 " ideal model delta sigma weight residual 110.72 102.97 7.75 1.69e+00 3.50e-01 2.10e+01 angle pdb=" C PHE F 497 " pdb=" N LYS F 498 " pdb=" CA LYS F 498 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" CA TYR C 328 " pdb=" C TYR C 328 " pdb=" N ARG C 329 " ideal model delta sigma weight residual 118.08 112.55 5.53 1.30e+00 5.92e-01 1.81e+01 ... (remaining 37202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 16502 34.84 - 69.68: 324 69.68 - 104.52: 39 104.52 - 139.36: 10 139.36 - 174.20: 3 Dihedral angle restraints: 16878 sinusoidal: 7107 harmonic: 9771 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.20 -174.20 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 79.50 -139.50 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 16875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3174 0.051 - 0.102: 902 0.102 - 0.154: 144 0.154 - 0.205: 19 0.205 - 0.256: 6 Chirality restraints: 4245 Sorted by residual: chirality pdb=" CB ILE C 550 " pdb=" CA ILE C 550 " pdb=" CG1 ILE C 550 " pdb=" CG2 ILE C 550 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 286 " pdb=" CA ILE A 286 " pdb=" CG1 ILE A 286 " pdb=" CG2 ILE A 286 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB THR A 665 " pdb=" CA THR A 665 " pdb=" OG1 THR A 665 " pdb=" CG2 THR A 665 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4242 not shown) Planarity restraints: 4825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 415 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.95e+01 pdb=" C MET F 415 " -0.094 2.00e-02 2.50e+03 pdb=" O MET F 415 " 0.035 2.00e-02 2.50e+03 pdb=" N THR F 416 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 328 " -0.026 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C TYR C 328 " 0.094 2.00e-02 2.50e+03 pdb=" O TYR C 328 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG C 329 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 494 " -0.055 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO C 495 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.046 5.00e-02 4.00e+02 ... (remaining 4822 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1410 2.73 - 3.27: 28518 3.27 - 3.81: 46961 3.81 - 4.36: 55647 4.36 - 4.90: 92400 Nonbonded interactions: 224936 Sorted by model distance: nonbonded pdb=" O ILE C 627 " pdb=" OH TYR C 635 " model vdw 2.183 3.040 nonbonded pdb=" O THR B 560 " pdb=" OG SER B 563 " model vdw 2.188 3.040 nonbonded pdb=" O ILE E 627 " pdb=" OH TYR E 635 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU C 288 " pdb=" NE2 HIS C 290 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN D 177 " pdb=" OG1 THR D 179 " model vdw 2.262 3.040 ... (remaining 224931 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 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 9 \ 01)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 901)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.003 0.045 27578 Z= 0.155 Angle : 0.813 12.435 37207 Z= 0.416 Chirality : 0.047 0.256 4245 Planarity : 0.006 0.084 4825 Dihedral : 15.186 174.199 10558 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3348 helix: -0.13 (0.12), residues: 1770 sheet: 0.01 (0.25), residues: 404 loop : 0.07 (0.20), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 646 TYR 0.026 0.002 TYR A 389 PHE 0.034 0.002 PHE B 551 TRP 0.016 0.002 TRP A 491 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00309 (27578) covalent geometry : angle 0.81261 (37207) hydrogen bonds : bond 0.16556 ( 1309) hydrogen bonds : angle 6.89640 ( 3840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9633 (mp) cc_final: 0.9409 (mp) REVERT: A 250 LEU cc_start: 0.9013 (tt) cc_final: 0.8332 (mt) REVERT: A 379 MET cc_start: 0.9127 (mpp) cc_final: 0.8624 (mpp) REVERT: B 198 GLU cc_start: 0.8982 (pt0) cc_final: 0.8773 (tp30) REVERT: B 622 VAL cc_start: 0.9256 (t) cc_final: 0.9038 (t) REVERT: C 227 GLU cc_start: 0.9245 (mp0) cc_final: 0.9021 (mp0) REVERT: C 274 LYS cc_start: 0.9293 (ttpt) cc_final: 0.8972 (tppt) REVERT: C 288 GLU cc_start: 0.7324 (tp30) cc_final: 0.6939 (tp30) REVERT: C 410 MET cc_start: 0.9329 (mmt) cc_final: 0.9111 (mmp) REVERT: C 579 GLN cc_start: 0.8253 (tm130) cc_final: 0.7997 (tm-30) REVERT: C 586 HIS cc_start: 0.8550 (p-80) cc_final: 0.8305 (p-80) REVERT: C 730 MET cc_start: 0.9117 (mmp) cc_final: 0.8840 (mmp) REVERT: D 201 MET cc_start: 0.8901 (mtp) cc_final: 0.8331 (mtm) REVERT: D 272 VAL cc_start: 0.8923 (t) cc_final: 0.8721 (p) REVERT: D 303 ASP cc_start: 0.8153 (p0) cc_final: 0.7934 (p0) REVERT: D 346 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8596 (mm110) REVERT: D 581 ASP cc_start: 0.9053 (m-30) cc_final: 0.8847 (m-30) REVERT: D 582 MET cc_start: 0.9029 (mmm) cc_final: 0.8579 (mmm) REVERT: D 627 ILE cc_start: 0.9348 (tp) cc_final: 0.9143 (tp) REVERT: D 638 LEU cc_start: 0.9491 (mp) cc_final: 0.9264 (mp) REVERT: D 656 ASP cc_start: 0.8968 (p0) cc_final: 0.8744 (p0) REVERT: E 183 MET cc_start: 0.9422 (ptp) cc_final: 0.8775 (ptp) REVERT: E 342 PHE cc_start: 0.9067 (m-80) cc_final: 0.8683 (m-80) REVERT: E 582 MET cc_start: 0.9438 (mmp) cc_final: 0.9129 (mmp) REVERT: E 616 ARG cc_start: 0.8927 (ptm160) cc_final: 0.8232 (tmm-80) REVERT: E 747 MET cc_start: 0.8419 (mtp) cc_final: 0.8093 (mtp) REVERT: F 201 MET cc_start: 0.8871 (mpp) cc_final: 0.8250 (mpp) REVERT: F 379 MET cc_start: 0.8720 (mpp) cc_final: 0.8420 (mpp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1702 time to fit residues: 92.3755 Evaluate side-chains 240 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 391 ASN C 579 GLN D 343 GLN D 370 HIS ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS E 490 ASN E 568 ASN ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 720 HIS F 290 HIS F 391 ASN F 515 HIS F 741 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053365 restraints weight = 164597.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054905 restraints weight = 102776.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056032 restraints weight = 72556.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056824 restraints weight = 55025.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057437 restraints weight = 44403.663| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27578 Z= 0.212 Angle : 0.664 7.235 37207 Z= 0.333 Chirality : 0.043 0.241 4245 Planarity : 0.005 0.063 4825 Dihedral : 9.138 176.487 3835 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3348 helix: 0.41 (0.12), residues: 1799 sheet: -0.20 (0.25), residues: 419 loop : 0.40 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 534 TYR 0.017 0.002 TYR C 604 PHE 0.030 0.002 PHE E 820 TRP 0.017 0.002 TRP F 491 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00426 (27578) covalent geometry : angle 0.66362 (37207) hydrogen bonds : bond 0.04022 ( 1309) hydrogen bonds : angle 5.46058 ( 3840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9752 (mp) cc_final: 0.9523 (mp) REVERT: A 250 LEU cc_start: 0.9198 (tt) cc_final: 0.8915 (tt) REVERT: A 379 MET cc_start: 0.9311 (mpp) cc_final: 0.8707 (mpp) REVERT: A 662 LEU cc_start: 0.9415 (mt) cc_final: 0.9097 (mt) REVERT: B 287 ASP cc_start: 0.9429 (m-30) cc_final: 0.9183 (m-30) REVERT: B 335 ASP cc_start: 0.9218 (t70) cc_final: 0.9016 (t0) REVERT: B 622 VAL cc_start: 0.9139 (t) cc_final: 0.8917 (t) REVERT: B 623 LEU cc_start: 0.9224 (tp) cc_final: 0.9003 (tp) REVERT: C 287 ASP cc_start: 0.8694 (t70) cc_final: 0.8270 (p0) REVERT: C 379 MET cc_start: 0.9031 (pmm) cc_final: 0.8802 (pmm) REVERT: C 410 MET cc_start: 0.9374 (mmt) cc_final: 0.9173 (mmp) REVERT: C 579 GLN cc_start: 0.8032 (tm130) cc_final: 0.7775 (tm-30) REVERT: C 730 MET cc_start: 0.9232 (mmp) cc_final: 0.8825 (mmp) REVERT: C 768 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6633 (mm) REVERT: D 201 MET cc_start: 0.9035 (mtp) cc_final: 0.8611 (mtm) REVERT: D 303 ASP cc_start: 0.8095 (p0) cc_final: 0.7764 (p0) REVERT: D 346 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8623 (mm110) REVERT: D 379 MET cc_start: 0.9358 (mpp) cc_final: 0.8728 (mpp) REVERT: D 582 MET cc_start: 0.9207 (mmm) cc_final: 0.8758 (mmm) REVERT: E 183 MET cc_start: 0.9257 (ptp) cc_final: 0.8702 (ptp) REVERT: E 342 PHE cc_start: 0.9142 (m-80) cc_final: 0.8703 (m-80) REVERT: E 582 MET cc_start: 0.9608 (mmp) cc_final: 0.9332 (mmm) REVERT: E 594 LEU cc_start: 0.8825 (tp) cc_final: 0.8619 (tt) REVERT: E 616 ARG cc_start: 0.9045 (ptm160) cc_final: 0.8209 (tmm-80) REVERT: E 623 LEU cc_start: 0.9723 (tt) cc_final: 0.9379 (tt) REVERT: E 730 MET cc_start: 0.9447 (mmm) cc_final: 0.9049 (tpt) REVERT: F 201 MET cc_start: 0.9070 (mpp) cc_final: 0.8633 (mpp) REVERT: F 379 MET cc_start: 0.8688 (mpp) cc_final: 0.8408 (mpp) REVERT: F 510 MET cc_start: 0.8898 (tmm) cc_final: 0.8366 (tmm) REVERT: F 551 PHE cc_start: 0.9482 (m-80) cc_final: 0.9221 (m-10) REVERT: F 582 MET cc_start: 0.7014 (mpp) cc_final: 0.6622 (mpp) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.1681 time to fit residues: 79.1940 Evaluate side-chains 212 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 87 optimal weight: 0.0770 chunk 327 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 251 optimal weight: 0.0070 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN D 636 ASN E 568 ASN F 290 HIS F 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054628 restraints weight = 162463.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056221 restraints weight = 100699.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057382 restraints weight = 70731.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058209 restraints weight = 53527.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058797 restraints weight = 42979.325| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27578 Z= 0.107 Angle : 0.603 9.006 37207 Z= 0.290 Chirality : 0.042 0.162 4245 Planarity : 0.004 0.061 4825 Dihedral : 8.735 174.830 3835 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3348 helix: 0.52 (0.12), residues: 1824 sheet: -0.17 (0.25), residues: 408 loop : 0.50 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 692 TYR 0.018 0.001 TYR A 331 PHE 0.028 0.001 PHE C 791 TRP 0.015 0.001 TRP F 491 HIS 0.002 0.000 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00229 (27578) covalent geometry : angle 0.60325 (37207) hydrogen bonds : bond 0.03346 ( 1309) hydrogen bonds : angle 5.05213 ( 3840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.006 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: A 178 LEU cc_start: 0.9745 (mp) cc_final: 0.9536 (mp) REVERT: A 250 LEU cc_start: 0.9139 (tt) cc_final: 0.8803 (tt) REVERT: A 270 LYS cc_start: 0.9757 (tmmt) cc_final: 0.9543 (pptt) REVERT: A 379 MET cc_start: 0.9376 (mpp) cc_final: 0.8691 (mpp) REVERT: B 287 ASP cc_start: 0.9373 (m-30) cc_final: 0.9072 (m-30) REVERT: B 335 ASP cc_start: 0.9192 (t70) cc_final: 0.8807 (t0) REVERT: B 338 LEU cc_start: 0.9417 (mt) cc_final: 0.8958 (mt) REVERT: B 379 MET cc_start: 0.8873 (pmm) cc_final: 0.8665 (pmm) REVERT: B 622 VAL cc_start: 0.9251 (t) cc_final: 0.9040 (t) REVERT: B 623 LEU cc_start: 0.9108 (tp) cc_final: 0.8905 (tp) REVERT: C 227 GLU cc_start: 0.9206 (mp0) cc_final: 0.8978 (mp0) REVERT: C 271 LYS cc_start: 0.9689 (tptt) cc_final: 0.9442 (tppt) REVERT: C 379 MET cc_start: 0.9049 (pmm) cc_final: 0.8778 (pmm) REVERT: C 410 MET cc_start: 0.9357 (mmt) cc_final: 0.9141 (mmp) REVERT: C 540 LYS cc_start: 0.9393 (pptt) cc_final: 0.8983 (pptt) REVERT: C 730 MET cc_start: 0.9155 (mmp) cc_final: 0.8807 (mmp) REVERT: C 747 MET cc_start: 0.8216 (mtt) cc_final: 0.7894 (mtt) REVERT: D 201 MET cc_start: 0.8946 (mtp) cc_final: 0.8586 (mtm) REVERT: D 244 ASP cc_start: 0.8658 (m-30) cc_final: 0.8353 (m-30) REVERT: D 272 VAL cc_start: 0.8972 (t) cc_final: 0.8770 (p) REVERT: D 288 GLU cc_start: 0.7683 (pp20) cc_final: 0.7376 (pp20) REVERT: D 303 ASP cc_start: 0.8011 (p0) cc_final: 0.7697 (p0) REVERT: D 346 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8535 (mm-40) REVERT: D 379 MET cc_start: 0.9324 (mpp) cc_final: 0.9103 (mpp) REVERT: D 582 MET cc_start: 0.8805 (mmm) cc_final: 0.8538 (mmm) REVERT: D 627 ILE cc_start: 0.9416 (tp) cc_final: 0.9190 (tp) REVERT: D 656 ASP cc_start: 0.8902 (p0) cc_final: 0.8679 (p0) REVERT: E 183 MET cc_start: 0.9270 (ptp) cc_final: 0.8620 (ptp) REVERT: E 342 PHE cc_start: 0.9087 (m-10) cc_final: 0.8678 (m-80) REVERT: E 582 MET cc_start: 0.9489 (mmp) cc_final: 0.9265 (mmm) REVERT: E 594 LEU cc_start: 0.8951 (tp) cc_final: 0.8737 (tt) REVERT: E 616 ARG cc_start: 0.9012 (ptm160) cc_final: 0.8217 (tmm-80) REVERT: E 623 LEU cc_start: 0.9685 (tt) cc_final: 0.9304 (tt) REVERT: F 200 VAL cc_start: 0.9451 (p) cc_final: 0.9152 (p) REVERT: F 201 MET cc_start: 0.9131 (mpp) cc_final: 0.8682 (mpp) REVERT: F 284 LEU cc_start: 0.9300 (tp) cc_final: 0.9093 (tp) REVERT: F 330 LYS cc_start: 0.9099 (ptmm) cc_final: 0.8792 (ptmm) REVERT: F 331 TYR cc_start: 0.8384 (m-80) cc_final: 0.7443 (m-80) REVERT: F 510 MET cc_start: 0.8968 (tmm) cc_final: 0.8369 (tmm) REVERT: F 551 PHE cc_start: 0.9440 (m-80) cc_final: 0.9165 (m-10) REVERT: F 582 MET cc_start: 0.7410 (mpp) cc_final: 0.7054 (mpp) REVERT: F 734 MET cc_start: 0.9135 (mpp) cc_final: 0.8821 (mmt) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1670 time to fit residues: 84.9353 Evaluate side-chains 228 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 63 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 chunk 310 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS C 391 ASN C 579 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 720 HIS F 290 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.066060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052813 restraints weight = 162079.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054366 restraints weight = 100612.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055464 restraints weight = 70687.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056295 restraints weight = 53701.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056864 restraints weight = 43103.805| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27578 Z= 0.140 Angle : 0.603 7.031 37207 Z= 0.293 Chirality : 0.042 0.239 4245 Planarity : 0.004 0.056 4825 Dihedral : 8.583 178.552 3835 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3348 helix: 0.68 (0.12), residues: 1816 sheet: -0.19 (0.24), residues: 437 loop : 0.69 (0.22), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 534 TYR 0.014 0.001 TYR D 331 PHE 0.029 0.001 PHE F 497 TRP 0.014 0.001 TRP F 491 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00296 (27578) covalent geometry : angle 0.60337 (37207) hydrogen bonds : bond 0.03182 ( 1309) hydrogen bonds : angle 4.95928 ( 3840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.037 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: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9332 (t-170) cc_final: 0.8997 (t-170) REVERT: A 379 MET cc_start: 0.9418 (mpp) cc_final: 0.8723 (mpp) REVERT: A 622 VAL cc_start: 0.8359 (t) cc_final: 0.8012 (p) REVERT: B 287 ASP cc_start: 0.9435 (m-30) cc_final: 0.9177 (m-30) REVERT: B 335 ASP cc_start: 0.9163 (t70) cc_final: 0.8750 (t0) REVERT: B 338 LEU cc_start: 0.9462 (mt) cc_final: 0.8955 (mt) REVERT: B 622 VAL cc_start: 0.9291 (t) cc_final: 0.9033 (t) REVERT: B 623 LEU cc_start: 0.9214 (tp) cc_final: 0.8405 (tp) REVERT: C 271 LYS cc_start: 0.9663 (tptt) cc_final: 0.9454 (tppt) REVERT: C 379 MET cc_start: 0.8926 (pmm) cc_final: 0.8636 (pmm) REVERT: C 410 MET cc_start: 0.9398 (mmt) cc_final: 0.9162 (mmp) REVERT: C 540 LYS cc_start: 0.9447 (pptt) cc_final: 0.9045 (pptt) REVERT: C 730 MET cc_start: 0.9160 (mmp) cc_final: 0.8815 (mmp) REVERT: C 747 MET cc_start: 0.8305 (mtt) cc_final: 0.8023 (mtt) REVERT: D 201 MET cc_start: 0.8953 (mtp) cc_final: 0.8607 (mtm) REVERT: D 244 ASP cc_start: 0.8562 (m-30) cc_final: 0.8224 (m-30) REVERT: D 272 VAL cc_start: 0.8977 (t) cc_final: 0.8775 (p) REVERT: D 303 ASP cc_start: 0.8071 (p0) cc_final: 0.7783 (p0) REVERT: D 379 MET cc_start: 0.9359 (mpp) cc_final: 0.9105 (mpp) REVERT: D 582 MET cc_start: 0.9201 (mmm) cc_final: 0.8753 (mmm) REVERT: D 656 ASP cc_start: 0.8922 (p0) cc_final: 0.8692 (p0) REVERT: E 215 ILE cc_start: 0.9272 (mp) cc_final: 0.8634 (tp) REVERT: E 342 PHE cc_start: 0.9078 (m-10) cc_final: 0.8694 (m-80) REVERT: E 582 MET cc_start: 0.9548 (mmp) cc_final: 0.9263 (mmm) REVERT: E 594 LEU cc_start: 0.9008 (tp) cc_final: 0.8770 (tt) REVERT: E 616 ARG cc_start: 0.9100 (ptm160) cc_final: 0.8345 (tmm-80) REVERT: E 623 LEU cc_start: 0.9730 (tt) cc_final: 0.9286 (tt) REVERT: E 747 MET cc_start: 0.7307 (mmp) cc_final: 0.6569 (mmm) REVERT: F 201 MET cc_start: 0.9051 (mpp) cc_final: 0.8621 (mpp) REVERT: F 284 LEU cc_start: 0.9332 (tp) cc_final: 0.9131 (tp) REVERT: F 289 LEU cc_start: 0.9594 (mm) cc_final: 0.9383 (mm) REVERT: F 330 LYS cc_start: 0.9102 (ptmm) cc_final: 0.8883 (ptmm) REVERT: F 331 TYR cc_start: 0.8400 (m-80) cc_final: 0.7398 (m-80) REVERT: F 510 MET cc_start: 0.9039 (tmm) cc_final: 0.8378 (tmm) REVERT: F 551 PHE cc_start: 0.9412 (m-80) cc_final: 0.9195 (m-10) REVERT: F 582 MET cc_start: 0.7452 (mpp) cc_final: 0.7095 (mpp) REVERT: F 734 MET cc_start: 0.9199 (mpp) cc_final: 0.8906 (mmm) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1720 time to fit residues: 82.0057 Evaluate side-chains 224 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 313 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN E 290 HIS E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053015 restraints weight = 162175.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054575 restraints weight = 100798.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055688 restraints weight = 70716.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056469 restraints weight = 53648.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057097 restraints weight = 43173.204| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27578 Z= 0.145 Angle : 0.614 9.266 37207 Z= 0.298 Chirality : 0.042 0.169 4245 Planarity : 0.004 0.058 4825 Dihedral : 8.404 176.711 3835 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1809 sheet: -0.30 (0.24), residues: 448 loop : 0.81 (0.22), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 534 TYR 0.024 0.001 TYR A 331 PHE 0.037 0.001 PHE C 791 TRP 0.017 0.001 TRP F 491 HIS 0.003 0.001 HIS D 515 Details of bonding type rmsd covalent geometry : bond 0.00306 (27578) covalent geometry : angle 0.61403 (37207) hydrogen bonds : bond 0.03138 ( 1309) hydrogen bonds : angle 4.91577 ( 3840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.052 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9730 (mp) cc_final: 0.9526 (mp) REVERT: A 331 TYR cc_start: 0.9085 (m-10) cc_final: 0.8755 (m-10) REVERT: A 354 HIS cc_start: 0.9326 (t-170) cc_final: 0.8968 (t-170) REVERT: A 379 MET cc_start: 0.9346 (mpp) cc_final: 0.8717 (mpp) REVERT: B 287 ASP cc_start: 0.9377 (m-30) cc_final: 0.9075 (m-30) REVERT: B 335 ASP cc_start: 0.9115 (t70) cc_final: 0.8713 (t0) REVERT: B 338 LEU cc_start: 0.9491 (mt) cc_final: 0.8915 (mt) REVERT: B 582 MET cc_start: 0.7967 (mmp) cc_final: 0.7689 (mmm) REVERT: B 623 LEU cc_start: 0.9063 (tp) cc_final: 0.8818 (tp) REVERT: C 287 ASP cc_start: 0.8677 (t0) cc_final: 0.8295 (p0) REVERT: C 290 HIS cc_start: 0.8249 (p90) cc_final: 0.7851 (p90) REVERT: C 379 MET cc_start: 0.9064 (pmm) cc_final: 0.8809 (pmm) REVERT: C 540 LYS cc_start: 0.9405 (pptt) cc_final: 0.9098 (pptt) REVERT: C 730 MET cc_start: 0.9156 (mmp) cc_final: 0.8899 (mmp) REVERT: C 747 MET cc_start: 0.8247 (mtt) cc_final: 0.7934 (mtt) REVERT: D 244 ASP cc_start: 0.8686 (m-30) cc_final: 0.8382 (m-30) REVERT: D 288 GLU cc_start: 0.8098 (pp20) cc_final: 0.7762 (pp20) REVERT: D 303 ASP cc_start: 0.8124 (p0) cc_final: 0.7853 (p0) REVERT: D 582 MET cc_start: 0.9236 (mmm) cc_final: 0.8806 (mmm) REVERT: D 656 ASP cc_start: 0.8887 (p0) cc_final: 0.8682 (p0) REVERT: E 215 ILE cc_start: 0.9134 (mp) cc_final: 0.8337 (tp) REVERT: E 329 ARG cc_start: 0.9087 (mtm110) cc_final: 0.8719 (mmm160) REVERT: E 342 PHE cc_start: 0.9050 (m-10) cc_final: 0.8556 (m-80) REVERT: E 582 MET cc_start: 0.9580 (mmp) cc_final: 0.9271 (mmm) REVERT: E 594 LEU cc_start: 0.9145 (tp) cc_final: 0.8875 (tt) REVERT: E 616 ARG cc_start: 0.9124 (ptm160) cc_final: 0.8308 (tmm-80) REVERT: E 623 LEU cc_start: 0.9738 (tt) cc_final: 0.9296 (tt) REVERT: E 747 MET cc_start: 0.7510 (mmp) cc_final: 0.7122 (mmm) REVERT: F 183 MET cc_start: 0.8707 (mmp) cc_final: 0.8499 (mmp) REVERT: F 201 MET cc_start: 0.9068 (mpp) cc_final: 0.8577 (mpp) REVERT: F 289 LEU cc_start: 0.9604 (mm) cc_final: 0.9361 (mm) REVERT: F 330 LYS cc_start: 0.9197 (ptmm) cc_final: 0.8970 (ptmm) REVERT: F 331 TYR cc_start: 0.8444 (m-80) cc_final: 0.7399 (m-80) REVERT: F 510 MET cc_start: 0.9059 (tmm) cc_final: 0.8415 (tmm) REVERT: F 551 PHE cc_start: 0.9409 (m-80) cc_final: 0.9099 (m-80) REVERT: F 582 MET cc_start: 0.7678 (mpp) cc_final: 0.7276 (mpp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1714 time to fit residues: 80.0527 Evaluate side-chains 227 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 228 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 132 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN D 290 HIS E 568 ASN E 631 HIS E 720 HIS F 290 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.066166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052977 restraints weight = 162579.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054541 restraints weight = 101153.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055663 restraints weight = 70731.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056469 restraints weight = 53466.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057065 restraints weight = 42892.103| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27578 Z= 0.129 Angle : 0.612 8.267 37207 Z= 0.296 Chirality : 0.042 0.183 4245 Planarity : 0.004 0.055 4825 Dihedral : 8.133 166.127 3835 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3348 helix: 0.74 (0.12), residues: 1811 sheet: -0.20 (0.24), residues: 430 loop : 0.78 (0.22), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 314 TYR 0.012 0.001 TYR A 331 PHE 0.035 0.001 PHE C 791 TRP 0.020 0.001 TRP F 491 HIS 0.003 0.001 HIS D 515 Details of bonding type rmsd covalent geometry : bond 0.00275 (27578) covalent geometry : angle 0.61232 (37207) hydrogen bonds : bond 0.03074 ( 1309) hydrogen bonds : angle 4.87158 ( 3840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.980 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: symmetry clash REVERT: A 354 HIS cc_start: 0.9237 (t-170) cc_final: 0.8975 (t-170) REVERT: A 379 MET cc_start: 0.9362 (mpp) cc_final: 0.8730 (mpp) REVERT: A 389 TYR cc_start: 0.7814 (m-10) cc_final: 0.7570 (m-10) REVERT: A 625 ASP cc_start: 0.8285 (t70) cc_final: 0.8034 (t70) REVERT: B 287 ASP cc_start: 0.9189 (m-30) cc_final: 0.8917 (m-30) REVERT: B 335 ASP cc_start: 0.9081 (t70) cc_final: 0.8676 (t0) REVERT: B 338 LEU cc_start: 0.9486 (mt) cc_final: 0.8909 (mt) REVERT: B 582 MET cc_start: 0.8065 (mmp) cc_final: 0.7828 (mmm) REVERT: B 623 LEU cc_start: 0.9070 (tp) cc_final: 0.8843 (tp) REVERT: B 640 GLN cc_start: 0.8429 (pp30) cc_final: 0.8138 (pp30) REVERT: B 647 LEU cc_start: 0.9218 (tp) cc_final: 0.9010 (tp) REVERT: C 287 ASP cc_start: 0.8689 (t0) cc_final: 0.8294 (p0) REVERT: C 288 GLU cc_start: 0.8119 (tp30) cc_final: 0.7414 (mm-30) REVERT: C 379 MET cc_start: 0.8971 (pmm) cc_final: 0.8711 (pmm) REVERT: C 510 MET cc_start: 0.9237 (ppp) cc_final: 0.9016 (ppp) REVERT: C 540 LYS cc_start: 0.9425 (pptt) cc_final: 0.9110 (pptt) REVERT: C 616 ARG cc_start: 0.8907 (mpt180) cc_final: 0.8632 (mmp80) REVERT: C 635 TYR cc_start: 0.8440 (m-80) cc_final: 0.8062 (m-80) REVERT: C 730 MET cc_start: 0.9154 (mmp) cc_final: 0.8912 (mmp) REVERT: C 747 MET cc_start: 0.8255 (mtt) cc_final: 0.7933 (mtt) REVERT: D 244 ASP cc_start: 0.8735 (m-30) cc_final: 0.8451 (m-30) REVERT: D 272 VAL cc_start: 0.8974 (t) cc_final: 0.8772 (p) REVERT: D 288 GLU cc_start: 0.8008 (pp20) cc_final: 0.7679 (pp20) REVERT: D 379 MET cc_start: 0.9402 (mpp) cc_final: 0.8931 (mpp) REVERT: D 582 MET cc_start: 0.9170 (mmm) cc_final: 0.8774 (mmm) REVERT: D 656 ASP cc_start: 0.8854 (p0) cc_final: 0.8622 (p0) REVERT: E 215 ILE cc_start: 0.8815 (mp) cc_final: 0.8321 (tp) REVERT: E 329 ARG cc_start: 0.9103 (mtm110) cc_final: 0.8724 (mmm160) REVERT: E 342 PHE cc_start: 0.9003 (m-10) cc_final: 0.8427 (m-80) REVERT: E 582 MET cc_start: 0.9557 (mmp) cc_final: 0.9282 (mmm) REVERT: E 594 LEU cc_start: 0.9175 (tp) cc_final: 0.8877 (tt) REVERT: E 616 ARG cc_start: 0.9156 (ptm160) cc_final: 0.8313 (tmm-80) REVERT: E 623 LEU cc_start: 0.9736 (tt) cc_final: 0.9370 (tt) REVERT: F 201 MET cc_start: 0.9038 (mpp) cc_final: 0.8538 (mpp) REVERT: F 284 LEU cc_start: 0.9316 (tp) cc_final: 0.9108 (tp) REVERT: F 289 LEU cc_start: 0.9606 (mm) cc_final: 0.9335 (mm) REVERT: F 330 LYS cc_start: 0.9199 (ptmm) cc_final: 0.8905 (ptmm) REVERT: F 331 TYR cc_start: 0.8466 (m-80) cc_final: 0.7451 (m-80) REVERT: F 510 MET cc_start: 0.9106 (tmm) cc_final: 0.8559 (tmm) REVERT: F 551 PHE cc_start: 0.9403 (m-80) cc_final: 0.9101 (m-80) REVERT: F 582 MET cc_start: 0.7478 (mpp) cc_final: 0.7076 (mpp) REVERT: F 734 MET cc_start: 0.9281 (mpp) cc_final: 0.8858 (mpp) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1603 time to fit residues: 77.4448 Evaluate side-chains 223 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 110 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 148 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 806 ASN D 290 HIS D 632 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS F 290 HIS ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051653 restraints weight = 164029.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053159 restraints weight = 102318.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054237 restraints weight = 71820.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054998 restraints weight = 54558.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055590 restraints weight = 44001.837| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27578 Z= 0.184 Angle : 0.653 8.425 37207 Z= 0.320 Chirality : 0.043 0.302 4245 Planarity : 0.004 0.055 4825 Dihedral : 7.907 150.328 3835 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3348 helix: 0.70 (0.12), residues: 1811 sheet: -0.38 (0.24), residues: 440 loop : 0.76 (0.22), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 314 TYR 0.018 0.002 TYR D 331 PHE 0.033 0.002 PHE C 791 TRP 0.023 0.002 TRP F 491 HIS 0.005 0.001 HIS D 515 Details of bonding type rmsd covalent geometry : bond 0.00386 (27578) covalent geometry : angle 0.65313 (37207) hydrogen bonds : bond 0.03253 ( 1309) hydrogen bonds : angle 4.97654 ( 3840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.838 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9428 (t-170) cc_final: 0.9050 (t-170) REVERT: A 379 MET cc_start: 0.9380 (mpp) cc_final: 0.8723 (mpp) REVERT: A 389 TYR cc_start: 0.7910 (m-10) cc_final: 0.7649 (m-10) REVERT: A 625 ASP cc_start: 0.8290 (t70) cc_final: 0.8073 (t70) REVERT: B 338 LEU cc_start: 0.9511 (mt) cc_final: 0.9264 (mt) REVERT: B 379 MET cc_start: 0.8970 (pmm) cc_final: 0.8691 (pmm) REVERT: B 623 LEU cc_start: 0.9141 (tp) cc_final: 0.8941 (tp) REVERT: B 640 GLN cc_start: 0.8621 (pp30) cc_final: 0.8265 (pp30) REVERT: B 693 MET cc_start: 0.7883 (pmm) cc_final: 0.7682 (pmm) REVERT: C 255 LEU cc_start: 0.9261 (mm) cc_final: 0.9053 (mm) REVERT: C 287 ASP cc_start: 0.8718 (t0) cc_final: 0.8403 (p0) REVERT: C 288 GLU cc_start: 0.8311 (tp30) cc_final: 0.7562 (mm-30) REVERT: C 290 HIS cc_start: 0.8511 (p90) cc_final: 0.7901 (p90) REVERT: C 379 MET cc_start: 0.9064 (pmm) cc_final: 0.8720 (pmm) REVERT: C 410 MET cc_start: 0.9158 (mmp) cc_final: 0.8797 (mmt) REVERT: C 540 LYS cc_start: 0.9510 (pptt) cc_final: 0.9200 (pptt) REVERT: C 730 MET cc_start: 0.9184 (mmp) cc_final: 0.8932 (mmp) REVERT: D 244 ASP cc_start: 0.8795 (m-30) cc_final: 0.8507 (m-30) REVERT: D 288 GLU cc_start: 0.8106 (pp20) cc_final: 0.7833 (pp20) REVERT: D 582 MET cc_start: 0.9283 (mmm) cc_final: 0.8843 (mmm) REVERT: D 656 ASP cc_start: 0.8898 (p0) cc_final: 0.8683 (p0) REVERT: E 183 MET cc_start: 0.9278 (ptp) cc_final: 0.8674 (ptp) REVERT: E 215 ILE cc_start: 0.8879 (mp) cc_final: 0.8266 (tp) REVERT: E 329 ARG cc_start: 0.9134 (mtm110) cc_final: 0.8742 (mmm160) REVERT: E 342 PHE cc_start: 0.9052 (m-10) cc_final: 0.8570 (m-80) REVERT: E 582 MET cc_start: 0.9604 (mmp) cc_final: 0.9285 (mmm) REVERT: E 616 ARG cc_start: 0.9153 (ptm160) cc_final: 0.8376 (tmm-80) REVERT: E 623 LEU cc_start: 0.9759 (tt) cc_final: 0.9283 (tt) REVERT: E 693 MET cc_start: 0.8174 (pmm) cc_final: 0.7938 (pmm) REVERT: F 201 MET cc_start: 0.9077 (mpp) cc_final: 0.8690 (mpp) REVERT: F 289 LEU cc_start: 0.9588 (mm) cc_final: 0.9271 (mm) REVERT: F 330 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8706 (ptmm) REVERT: F 331 TYR cc_start: 0.8420 (m-80) cc_final: 0.7474 (m-80) REVERT: F 510 MET cc_start: 0.9143 (tmm) cc_final: 0.8611 (tmm) REVERT: F 551 PHE cc_start: 0.9352 (m-80) cc_final: 0.9084 (m-80) REVERT: F 648 THR cc_start: 0.8707 (m) cc_final: 0.8482 (p) REVERT: F 734 MET cc_start: 0.9271 (mpp) cc_final: 0.8913 (mpp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1657 time to fit residues: 75.8936 Evaluate side-chains 216 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 329 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 579 GLN E 568 ASN E 631 HIS F 290 HIS ** F 640 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 = 0.3396 r_free = 0.3396 target = 0.065731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052540 restraints weight = 162103.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054069 restraints weight = 100888.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055151 restraints weight = 70845.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055981 restraints weight = 53718.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056559 restraints weight = 43059.534| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27578 Z= 0.122 Angle : 0.629 8.362 37207 Z= 0.304 Chirality : 0.043 0.234 4245 Planarity : 0.004 0.111 4825 Dihedral : 7.758 149.452 3835 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1815 sheet: -0.27 (0.24), residues: 438 loop : 0.82 (0.22), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 712 TYR 0.021 0.002 TYR A 328 PHE 0.031 0.001 PHE C 791 TRP 0.023 0.001 TRP F 491 HIS 0.006 0.001 HIS C 631 Details of bonding type rmsd covalent geometry : bond 0.00265 (27578) covalent geometry : angle 0.62907 (37207) hydrogen bonds : bond 0.03045 ( 1309) hydrogen bonds : angle 4.91007 ( 3840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.970 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.9080 (m-10) cc_final: 0.8861 (m-10) REVERT: A 354 HIS cc_start: 0.9261 (t-170) cc_final: 0.8943 (t-170) REVERT: A 379 MET cc_start: 0.9371 (mpp) cc_final: 0.8704 (mpp) REVERT: A 389 TYR cc_start: 0.7943 (m-10) cc_final: 0.7619 (m-10) REVERT: A 622 VAL cc_start: 0.8689 (t) cc_final: 0.8297 (p) REVERT: A 625 ASP cc_start: 0.8224 (t70) cc_final: 0.8005 (t70) REVERT: B 338 LEU cc_start: 0.9496 (mt) cc_final: 0.9246 (mt) REVERT: B 582 MET cc_start: 0.8074 (mmp) cc_final: 0.7825 (mmm) REVERT: B 623 LEU cc_start: 0.9067 (tp) cc_final: 0.8857 (tp) REVERT: B 693 MET cc_start: 0.7611 (pmm) cc_final: 0.7401 (pmm) REVERT: C 227 GLU cc_start: 0.9256 (mp0) cc_final: 0.9011 (mp0) REVERT: C 271 LYS cc_start: 0.9650 (tptt) cc_final: 0.9444 (tppt) REVERT: C 287 ASP cc_start: 0.8656 (t0) cc_final: 0.8301 (p0) REVERT: C 288 GLU cc_start: 0.8174 (tp30) cc_final: 0.7622 (mm-30) REVERT: C 290 HIS cc_start: 0.8428 (p90) cc_final: 0.7912 (p90) REVERT: C 379 MET cc_start: 0.9007 (pmm) cc_final: 0.8603 (pmm) REVERT: C 410 MET cc_start: 0.9256 (mmp) cc_final: 0.8873 (mmt) REVERT: C 540 LYS cc_start: 0.9435 (pptt) cc_final: 0.9108 (pptt) REVERT: C 635 TYR cc_start: 0.8020 (m-80) cc_final: 0.7664 (m-80) REVERT: C 693 MET cc_start: 0.8082 (pmm) cc_final: 0.7877 (pmm) REVERT: C 747 MET cc_start: 0.8213 (mtt) cc_final: 0.7545 (mtt) REVERT: D 244 ASP cc_start: 0.8764 (m-30) cc_final: 0.8449 (m-30) REVERT: D 272 VAL cc_start: 0.8978 (t) cc_final: 0.8771 (p) REVERT: D 288 GLU cc_start: 0.7959 (pp20) cc_final: 0.7520 (pp20) REVERT: D 582 MET cc_start: 0.9131 (mmm) cc_final: 0.8758 (mmm) REVERT: D 627 ILE cc_start: 0.9373 (tp) cc_final: 0.9159 (tp) REVERT: D 656 ASP cc_start: 0.8819 (p0) cc_final: 0.8598 (p0) REVERT: E 215 ILE cc_start: 0.8764 (mp) cc_final: 0.8137 (tp) REVERT: E 332 ILE cc_start: 0.9053 (mt) cc_final: 0.8669 (mt) REVERT: E 342 PHE cc_start: 0.8923 (m-10) cc_final: 0.8491 (m-80) REVERT: E 582 MET cc_start: 0.9561 (mmp) cc_final: 0.9276 (mmm) REVERT: E 594 LEU cc_start: 0.9263 (tp) cc_final: 0.8979 (tt) REVERT: E 616 ARG cc_start: 0.9152 (ptm160) cc_final: 0.8390 (tmm-80) REVERT: E 623 LEU cc_start: 0.9757 (tt) cc_final: 0.9396 (tt) REVERT: F 201 MET cc_start: 0.9021 (mpp) cc_final: 0.8571 (mpp) REVERT: F 284 LEU cc_start: 0.9340 (tp) cc_final: 0.9139 (tp) REVERT: F 289 LEU cc_start: 0.9580 (mm) cc_final: 0.9236 (mm) REVERT: F 330 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8651 (ptmm) REVERT: F 331 TYR cc_start: 0.8477 (m-80) cc_final: 0.7652 (m-80) REVERT: F 510 MET cc_start: 0.9144 (tmm) cc_final: 0.8741 (tmm) REVERT: F 551 PHE cc_start: 0.9355 (m-80) cc_final: 0.9069 (m-80) REVERT: F 582 MET cc_start: 0.7342 (mpp) cc_final: 0.6944 (mpp) REVERT: F 648 THR cc_start: 0.8694 (m) cc_final: 0.8470 (p) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1661 time to fit residues: 76.7826 Evaluate side-chains 222 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 26 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 287 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 695 GLN D 290 HIS E 568 ASN E 631 HIS F 290 HIS ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052021 restraints weight = 159979.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053572 restraints weight = 99446.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054662 restraints weight = 69604.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055498 restraints weight = 52691.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056080 restraints weight = 42177.010| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27578 Z= 0.126 Angle : 0.641 10.183 37207 Z= 0.311 Chirality : 0.043 0.222 4245 Planarity : 0.004 0.067 4825 Dihedral : 7.635 148.728 3835 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3348 helix: 0.70 (0.12), residues: 1818 sheet: -0.24 (0.24), residues: 439 loop : 0.80 (0.22), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 588 TYR 0.020 0.002 TYR A 328 PHE 0.033 0.001 PHE F 497 TRP 0.024 0.001 TRP F 491 HIS 0.005 0.001 HIS C 631 Details of bonding type rmsd covalent geometry : bond 0.00275 (27578) covalent geometry : angle 0.64113 (37207) hydrogen bonds : bond 0.03091 ( 1309) hydrogen bonds : angle 4.93989 ( 3840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.994 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.9143 (m-10) cc_final: 0.8934 (m-10) REVERT: A 354 HIS cc_start: 0.9362 (t-170) cc_final: 0.8957 (t-170) REVERT: A 379 MET cc_start: 0.9397 (mpp) cc_final: 0.8679 (mpp) REVERT: A 389 TYR cc_start: 0.8000 (m-10) cc_final: 0.7674 (m-10) REVERT: A 622 VAL cc_start: 0.8730 (t) cc_final: 0.8433 (p) REVERT: B 287 ASP cc_start: 0.9526 (m-30) cc_final: 0.9310 (m-30) REVERT: B 288 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 338 LEU cc_start: 0.9501 (mt) cc_final: 0.9254 (mt) REVERT: B 379 MET cc_start: 0.8747 (pmm) cc_final: 0.8520 (pmm) REVERT: B 582 MET cc_start: 0.8089 (mmp) cc_final: 0.7836 (mmm) REVERT: B 623 LEU cc_start: 0.9086 (tp) cc_final: 0.8873 (tp) REVERT: B 693 MET cc_start: 0.7636 (pmm) cc_final: 0.7428 (pmm) REVERT: C 227 GLU cc_start: 0.9240 (mp0) cc_final: 0.8957 (mp0) REVERT: C 271 LYS cc_start: 0.9661 (tptt) cc_final: 0.9422 (tptp) REVERT: C 287 ASP cc_start: 0.8654 (t0) cc_final: 0.8302 (p0) REVERT: C 288 GLU cc_start: 0.8224 (tp30) cc_final: 0.7789 (mm-30) REVERT: C 290 HIS cc_start: 0.8530 (p90) cc_final: 0.8327 (p-80) REVERT: C 379 MET cc_start: 0.9026 (pmm) cc_final: 0.8625 (pmm) REVERT: C 540 LYS cc_start: 0.9434 (pptt) cc_final: 0.9100 (pptt) REVERT: C 635 TYR cc_start: 0.8072 (m-80) cc_final: 0.7670 (m-80) REVERT: C 693 MET cc_start: 0.8109 (pmm) cc_final: 0.7893 (pmm) REVERT: C 730 MET cc_start: 0.9152 (mmp) cc_final: 0.8917 (mmp) REVERT: D 244 ASP cc_start: 0.8820 (m-30) cc_final: 0.8504 (m-30) REVERT: D 272 VAL cc_start: 0.8992 (t) cc_final: 0.8787 (p) REVERT: D 288 GLU cc_start: 0.8018 (pp20) cc_final: 0.7605 (pp20) REVERT: D 290 HIS cc_start: 0.9116 (p90) cc_final: 0.8846 (p-80) REVERT: D 415 MET cc_start: 0.7718 (pmm) cc_final: 0.7293 (pmm) REVERT: D 582 MET cc_start: 0.9182 (mmm) cc_final: 0.8799 (mmm) REVERT: D 656 ASP cc_start: 0.8873 (p0) cc_final: 0.8660 (p0) REVERT: E 215 ILE cc_start: 0.8775 (mp) cc_final: 0.8031 (tp) REVERT: E 291 THR cc_start: 0.9276 (p) cc_final: 0.8942 (p) REVERT: E 328 TYR cc_start: 0.9247 (t80) cc_final: 0.7924 (t80) REVERT: E 329 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8735 (mmm160) REVERT: E 342 PHE cc_start: 0.8907 (m-10) cc_final: 0.8468 (m-80) REVERT: E 582 MET cc_start: 0.9578 (mmp) cc_final: 0.9286 (mmm) REVERT: E 594 LEU cc_start: 0.9264 (tp) cc_final: 0.8976 (tp) REVERT: E 616 ARG cc_start: 0.9187 (ptm160) cc_final: 0.8454 (tmm-80) REVERT: E 623 LEU cc_start: 0.9765 (tt) cc_final: 0.9393 (tt) REVERT: F 201 MET cc_start: 0.9011 (mpp) cc_final: 0.8567 (mpp) REVERT: F 284 LEU cc_start: 0.9343 (tp) cc_final: 0.9134 (tp) REVERT: F 289 LEU cc_start: 0.9557 (mm) cc_final: 0.9354 (mm) REVERT: F 330 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8690 (ptmm) REVERT: F 331 TYR cc_start: 0.8499 (m-80) cc_final: 0.7834 (m-80) REVERT: F 510 MET cc_start: 0.9218 (tmm) cc_final: 0.8804 (tmm) REVERT: F 551 PHE cc_start: 0.9339 (m-80) cc_final: 0.9057 (m-80) REVERT: F 582 MET cc_start: 0.7301 (mpp) cc_final: 0.6950 (mpp) REVERT: F 734 MET cc_start: 0.9203 (mpp) cc_final: 0.8570 (mpp) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1679 time to fit residues: 77.4624 Evaluate side-chains 218 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 276 optimal weight: 0.1980 chunk 233 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 141 optimal weight: 0.7980 chunk 322 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 343 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 651 GLN E 568 ASN E 631 HIS F 290 HIS F 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053845 restraints weight = 158630.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055437 restraints weight = 98131.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056599 restraints weight = 68301.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057426 restraints weight = 51193.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.058025 restraints weight = 40770.075| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27578 Z= 0.108 Angle : 0.646 9.877 37207 Z= 0.310 Chirality : 0.043 0.220 4245 Planarity : 0.004 0.055 4825 Dihedral : 7.409 147.490 3835 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3348 helix: 0.70 (0.12), residues: 1826 sheet: -0.09 (0.25), residues: 423 loop : 0.73 (0.21), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 314 TYR 0.020 0.001 TYR A 328 PHE 0.030 0.001 PHE C 791 TRP 0.026 0.001 TRP F 491 HIS 0.006 0.001 HIS E 354 Details of bonding type rmsd covalent geometry : bond 0.00234 (27578) covalent geometry : angle 0.64571 (37207) hydrogen bonds : bond 0.02995 ( 1309) hydrogen bonds : angle 4.85301 ( 3840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.038 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9696 (mp) cc_final: 0.9475 (mp) REVERT: A 331 TYR cc_start: 0.9118 (m-10) cc_final: 0.8862 (m-10) REVERT: A 354 HIS cc_start: 0.9302 (t-170) cc_final: 0.8920 (t-170) REVERT: A 379 MET cc_start: 0.9395 (mpp) cc_final: 0.8688 (mpp) REVERT: A 389 TYR cc_start: 0.8030 (m-10) cc_final: 0.7667 (m-10) REVERT: A 582 MET cc_start: 0.7433 (mpp) cc_final: 0.7088 (mpp) REVERT: A 622 VAL cc_start: 0.8688 (t) cc_final: 0.8487 (p) REVERT: A 625 ASP cc_start: 0.8569 (t70) cc_final: 0.8079 (t0) REVERT: B 198 GLU cc_start: 0.9127 (pt0) cc_final: 0.8834 (tp30) REVERT: B 287 ASP cc_start: 0.9486 (m-30) cc_final: 0.9266 (m-30) REVERT: B 288 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7634 (tp30) REVERT: B 338 LEU cc_start: 0.9442 (mt) cc_final: 0.9201 (mt) REVERT: C 227 GLU cc_start: 0.9399 (mp0) cc_final: 0.9045 (pm20) REVERT: C 287 ASP cc_start: 0.8557 (t0) cc_final: 0.8215 (p0) REVERT: C 288 GLU cc_start: 0.8005 (tp30) cc_final: 0.7509 (mm-30) REVERT: C 333 GLU cc_start: 0.8500 (tt0) cc_final: 0.8139 (tp30) REVERT: C 379 MET cc_start: 0.9106 (pmm) cc_final: 0.8660 (pmm) REVERT: C 410 MET cc_start: 0.9117 (mmp) cc_final: 0.8884 (mmt) REVERT: C 540 LYS cc_start: 0.9434 (pptt) cc_final: 0.9095 (pptt) REVERT: C 616 ARG cc_start: 0.8884 (mpt180) cc_final: 0.8638 (mmp80) REVERT: C 635 TYR cc_start: 0.8225 (m-80) cc_final: 0.7947 (m-80) REVERT: D 244 ASP cc_start: 0.8777 (m-30) cc_final: 0.8448 (m-30) REVERT: D 288 GLU cc_start: 0.7747 (pp20) cc_final: 0.7254 (pp20) REVERT: D 290 HIS cc_start: 0.9020 (p90) cc_final: 0.8707 (p-80) REVERT: D 415 MET cc_start: 0.7647 (pmm) cc_final: 0.7400 (pmm) REVERT: D 582 MET cc_start: 0.8933 (mmm) cc_final: 0.8586 (mmm) REVERT: D 656 ASP cc_start: 0.8846 (p0) cc_final: 0.8611 (p0) REVERT: E 215 ILE cc_start: 0.8691 (mp) cc_final: 0.7859 (tp) REVERT: E 291 THR cc_start: 0.9280 (p) cc_final: 0.9066 (p) REVERT: E 328 TYR cc_start: 0.9243 (t80) cc_final: 0.7745 (t80) REVERT: E 329 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8589 (mmm160) REVERT: E 342 PHE cc_start: 0.8841 (m-10) cc_final: 0.8391 (m-80) REVERT: E 582 MET cc_start: 0.9521 (mmp) cc_final: 0.9231 (mmm) REVERT: E 594 LEU cc_start: 0.9279 (tp) cc_final: 0.8979 (tt) REVERT: E 616 ARG cc_start: 0.9156 (ptm160) cc_final: 0.8421 (tmm-80) REVERT: E 623 LEU cc_start: 0.9754 (tt) cc_final: 0.9360 (tt) REVERT: F 201 MET cc_start: 0.8931 (mpp) cc_final: 0.8480 (mpp) REVERT: F 330 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8635 (ptmm) REVERT: F 331 TYR cc_start: 0.8510 (m-80) cc_final: 0.7767 (m-80) REVERT: F 379 MET cc_start: 0.8608 (ppp) cc_final: 0.8292 (ppp) REVERT: F 510 MET cc_start: 0.9165 (tmm) cc_final: 0.8718 (tmm) REVERT: F 551 PHE cc_start: 0.9312 (m-80) cc_final: 0.9025 (m-80) REVERT: F 582 MET cc_start: 0.7403 (mpp) cc_final: 0.7082 (mpp) REVERT: F 734 MET cc_start: 0.9131 (mpp) cc_final: 0.8674 (mpp) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.1687 time to fit residues: 80.1746 Evaluate side-chains 228 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 333 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 343 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN E 568 ASN E 631 HIS F 290 HIS ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.052144 restraints weight = 161042.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053681 restraints weight = 99804.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054790 restraints weight = 69684.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055571 restraints weight = 52483.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056183 restraints weight = 42103.558| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27578 Z= 0.153 Angle : 0.655 9.118 37207 Z= 0.320 Chirality : 0.043 0.222 4245 Planarity : 0.004 0.054 4825 Dihedral : 7.388 145.760 3835 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1830 sheet: -0.27 (0.24), residues: 461 loop : 0.81 (0.22), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 712 TYR 0.021 0.002 TYR D 331 PHE 0.045 0.001 PHE F 497 TRP 0.024 0.002 TRP F 491 HIS 0.003 0.001 HIS C 631 Details of bonding type rmsd covalent geometry : bond 0.00325 (27578) covalent geometry : angle 0.65548 (37207) hydrogen bonds : bond 0.03127 ( 1309) hydrogen bonds : angle 4.90170 ( 3840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.77 seconds wall clock time: 68 minutes 15.61 seconds (4095.61 seconds total)