Starting phenix.real_space_refine on Sun May 25 23:48:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_15242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_15242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_15242.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_15242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8w_15242/05_2025/8a8w_15242.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.23, per 1000 atoms: 0.56 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: 6.09 Conformation dependent library (CDL) restraints added in 3.6 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: 3.23 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: 9.30 Time building geometry restraints manager: 7.12 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 8 \ 21 or resid 901)) 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 821 or resid 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 821 or resid 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 821 or resid 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 821 or resid 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 821 or resid 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: 0.870 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: 0.870 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 56.110 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP A 491 HIS 0.007 0.001 HIS C 290 PHE 0.034 0.002 PHE B 551 TYR 0.026 0.002 TYR A 389 ARG 0.011 0.000 ARG E 646 Details of bonding type rmsd hydrogen bonds : bond 0.16556 ( 1309) hydrogen bonds : angle 6.89640 ( 3840) covalent geometry : bond 0.00309 (27578) covalent geometry : angle 0.81261 (37207) *********************** 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 : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9633 (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: B 815 ASP cc_start: 0.9005 (m-30) cc_final: 0.8687 (t0) 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: 0.6940 (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: 0.7996 (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: 0.7935 (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: 0.8849 (m-30) REVERT: D 582 MET cc_start: 0.9029 (mmm) cc_final: 0.8577 (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: 0.8249 (mpp) REVERT: F 379 MET cc_start: 0.8720 (mpp) cc_final: 0.8421 (mpp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3764 time to fit residues: 203.2780 Evaluate side-chains 243 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 142 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 264 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 306 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 GLN C 579 GLN C 695 GLN D 636 ASN E 568 ASN ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 720 HIS F 290 HIS F 391 ASN F 667 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.069271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055718 restraints weight = 155771.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057369 restraints weight = 96787.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058545 restraints weight = 67900.836| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27578 Z= 0.110 Angle : 0.612 8.022 37207 Z= 0.298 Chirality : 0.042 0.220 4245 Planarity : 0.004 0.068 4825 Dihedral : 8.852 173.425 3835 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3348 helix: 0.38 (0.12), residues: 1805 sheet: -0.05 (0.25), residues: 419 loop : 0.30 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 491 HIS 0.004 0.001 HIS C 370 PHE 0.033 0.001 PHE F 497 TYR 0.016 0.001 TYR A 331 ARG 0.006 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1309) hydrogen bonds : angle 5.24424 ( 3840) covalent geometry : bond 0.00228 (27578) covalent geometry : angle 0.61174 (37207) *********************** 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 320 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 3.125 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: 0.9704 (mp) cc_final: 0.9429 (mp) REVERT: A 250 LEU cc_start: 0.9062 (tt) cc_final: 0.8479 (mm) REVERT: A 379 MET cc_start: 0.9281 (mpp) cc_final: 0.8710 (mpp) REVERT: A 389 TYR cc_start: 0.8036 (m-10) cc_final: 0.7835 (m-10) REVERT: A 662 LEU cc_start: 0.9417 (mt) cc_final: 0.9162 (mt) REVERT: B 287 ASP cc_start: 0.9388 (m-30) cc_final: 0.9125 (m-30) REVERT: B 335 ASP cc_start: 0.9356 (t70) cc_final: 0.9012 (t0) REVERT: B 338 LEU cc_start: 0.9378 (mt) cc_final: 0.8923 (mt) REVERT: B 622 VAL cc_start: 0.9166 (t) cc_final: 0.8932 (t) REVERT: C 227 GLU cc_start: 0.9339 (mp0) cc_final: 0.9101 (mp0) REVERT: C 379 MET cc_start: 0.9198 (pmm) cc_final: 0.8946 (pmm) REVERT: C 410 MET cc_start: 0.9404 (mmt) cc_final: 0.9185 (mmp) REVERT: C 579 GLN cc_start: 0.7985 (tm130) cc_final: 0.7751 (tm-30) REVERT: C 693 MET cc_start: 0.8251 (pmm) cc_final: 0.8002 (pmm) REVERT: C 730 MET cc_start: 0.9196 (mmp) cc_final: 0.8890 (mmp) REVERT: D 201 MET cc_start: 0.9010 (mtp) cc_final: 0.8553 (mtm) REVERT: D 233 ILE cc_start: 0.9388 (mt) cc_final: 0.9126 (tt) REVERT: D 244 ASP cc_start: 0.8629 (m-30) cc_final: 0.8294 (m-30) REVERT: D 303 ASP cc_start: 0.7860 (p0) cc_final: 0.7463 (p0) REVERT: D 346 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8652 (mm-40) REVERT: D 379 MET cc_start: 0.9261 (mpp) cc_final: 0.8642 (mpp) REVERT: D 582 MET cc_start: 0.8836 (mmm) cc_final: 0.8541 (mmm) REVERT: D 627 ILE cc_start: 0.9466 (tp) cc_final: 0.9258 (tp) REVERT: D 638 LEU cc_start: 0.9463 (mp) cc_final: 0.9246 (mp) REVERT: D 656 ASP cc_start: 0.8989 (p0) cc_final: 0.8788 (p0) REVERT: D 730 MET cc_start: 0.9014 (tpp) cc_final: 0.8654 (tpp) REVERT: E 183 MET cc_start: 0.9300 (ptp) cc_final: 0.8697 (ptp) REVERT: E 342 PHE cc_start: 0.9129 (m-80) cc_final: 0.8698 (m-80) REVERT: E 357 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8646 (mm-30) REVERT: E 582 MET cc_start: 0.9448 (mmp) cc_final: 0.9223 (mmm) REVERT: E 616 ARG cc_start: 0.9024 (ptm160) cc_final: 0.8156 (tmm-80) REVERT: E 623 LEU cc_start: 0.9659 (tt) cc_final: 0.9363 (tt) REVERT: E 656 ASP cc_start: 0.9498 (p0) cc_final: 0.9291 (p0) REVERT: F 200 VAL cc_start: 0.9422 (p) cc_final: 0.9061 (p) REVERT: F 201 MET cc_start: 0.8925 (mpp) cc_final: 0.8443 (mpp) REVERT: F 379 MET cc_start: 0.8689 (mpp) cc_final: 0.8405 (mpp) REVERT: F 510 MET cc_start: 0.8880 (tmm) cc_final: 0.8308 (tmm) REVERT: F 551 PHE cc_start: 0.9425 (m-80) cc_final: 0.9109 (m-10) REVERT: F 582 MET cc_start: 0.7370 (mpp) cc_final: 0.7050 (mpp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.3547 time to fit residues: 185.7553 Evaluate side-chains 233 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 260 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 315 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS C 343 GLN C 391 ASN C 579 GLN D 370 HIS D 711 ASN E 568 ASN F 290 HIS F 515 HIS F 741 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.067078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.053764 restraints weight = 161651.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055349 restraints weight = 100506.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056489 restraints weight = 70344.212| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27578 Z= 0.161 Angle : 0.616 8.619 37207 Z= 0.301 Chirality : 0.042 0.186 4245 Planarity : 0.004 0.060 4825 Dihedral : 8.667 175.370 3835 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3348 helix: 0.56 (0.12), residues: 1826 sheet: -0.11 (0.25), residues: 427 loop : 0.47 (0.21), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 491 HIS 0.005 0.001 HIS C 290 PHE 0.026 0.001 PHE C 791 TYR 0.014 0.001 TYR B 635 ARG 0.007 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 1309) hydrogen bonds : angle 5.07472 ( 3840) covalent geometry : bond 0.00334 (27578) covalent geometry : angle 0.61584 (37207) *********************** 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 290 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 287 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9690 (mp) cc_final: 0.9469 (mp) REVERT: A 250 LEU cc_start: 0.9149 (tt) cc_final: 0.8824 (tt) REVERT: A 379 MET cc_start: 0.9390 (mpp) cc_final: 0.8749 (mpp) REVERT: A 389 TYR cc_start: 0.8014 (m-10) cc_final: 0.7702 (m-10) REVERT: B 287 ASP cc_start: 0.9438 (m-30) cc_final: 0.9162 (m-30) REVERT: B 335 ASP cc_start: 0.9195 (t70) cc_final: 0.8774 (t0) REVERT: B 338 LEU cc_start: 0.9431 (mt) cc_final: 0.8946 (mt) REVERT: B 379 MET cc_start: 0.8952 (pmm) cc_final: 0.8728 (pmm) REVERT: B 622 VAL cc_start: 0.9239 (t) cc_final: 0.9018 (t) REVERT: B 623 LEU cc_start: 0.9221 (tp) cc_final: 0.9014 (tp) REVERT: C 379 MET cc_start: 0.8994 (pmm) cc_final: 0.8774 (pmm) REVERT: C 410 MET cc_start: 0.9409 (mmt) cc_final: 0.9190 (mmp) REVERT: C 730 MET cc_start: 0.9242 (mmp) cc_final: 0.8865 (mmp) REVERT: D 201 MET cc_start: 0.8991 (mtp) cc_final: 0.8599 (mtm) REVERT: D 244 ASP cc_start: 0.8548 (m-30) cc_final: 0.8157 (m-30) REVERT: D 288 GLU cc_start: 0.7892 (pp20) cc_final: 0.7614 (pp20) REVERT: D 303 ASP cc_start: 0.8056 (p0) cc_final: 0.7773 (p0) REVERT: D 346 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8584 (mm-40) REVERT: D 379 MET cc_start: 0.9344 (mpp) cc_final: 0.9104 (mpp) REVERT: D 392 ASP cc_start: 0.7733 (t0) cc_final: 0.7477 (t0) REVERT: D 582 MET cc_start: 0.9151 (mmm) cc_final: 0.8734 (mmm) REVERT: E 183 MET cc_start: 0.9285 (ptp) cc_final: 0.8680 (ptp) REVERT: E 215 ILE cc_start: 0.9085 (mp) cc_final: 0.8392 (tp) REVERT: E 342 PHE cc_start: 0.9120 (m-80) cc_final: 0.8696 (m-80) REVERT: E 582 MET cc_start: 0.9581 (mmp) cc_final: 0.9290 (mmm) REVERT: E 594 LEU cc_start: 0.8953 (tp) cc_final: 0.8599 (tt) REVERT: E 616 ARG cc_start: 0.9022 (ptm160) cc_final: 0.8262 (tmm-80) REVERT: E 623 LEU cc_start: 0.9695 (tt) cc_final: 0.9312 (tt) REVERT: E 747 MET cc_start: 0.8545 (mtt) cc_final: 0.8345 (mmm) REVERT: F 201 MET cc_start: 0.9115 (mpp) cc_final: 0.8648 (mpp) REVERT: F 510 MET cc_start: 0.8969 (tmm) cc_final: 0.8428 (tmm) REVERT: F 551 PHE cc_start: 0.9424 (m-80) cc_final: 0.9166 (m-10) REVERT: F 582 MET cc_start: 0.7427 (mpp) cc_final: 0.7089 (mpp) outliers start: 3 outliers final: 0 residues processed: 289 average time/residue: 0.3843 time to fit residues: 183.4610 Evaluate side-chains 215 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 336 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** B 640 GLN C 391 ASN C 579 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS 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 = 0.066273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.053086 restraints weight = 165120.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.054661 restraints weight = 102484.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055763 restraints weight = 71420.461| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27578 Z= 0.150 Angle : 0.616 7.157 37207 Z= 0.300 Chirality : 0.042 0.232 4245 Planarity : 0.004 0.061 4825 Dihedral : 8.549 178.798 3835 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3348 helix: 0.62 (0.12), residues: 1822 sheet: -0.12 (0.24), residues: 444 loop : 0.66 (0.22), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 491 HIS 0.004 0.001 HIS E 631 PHE 0.031 0.001 PHE F 497 TYR 0.019 0.001 TYR A 331 ARG 0.005 0.000 ARG D 615 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 1309) hydrogen bonds : angle 4.96403 ( 3840) covalent geometry : bond 0.00312 (27578) covalent geometry : angle 0.61622 (37207) *********************** 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 292 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9326 (t-170) cc_final: 0.8999 (t-170) REVERT: A 379 MET cc_start: 0.9413 (mpp) cc_final: 0.8736 (mpp) REVERT: A 389 TYR cc_start: 0.8010 (m-10) cc_final: 0.7627 (m-10) REVERT: B 287 ASP cc_start: 0.9469 (m-30) cc_final: 0.9193 (m-30) REVERT: B 288 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 335 ASP cc_start: 0.9162 (t70) cc_final: 0.8769 (t0) REVERT: B 338 LEU cc_start: 0.9460 (mt) cc_final: 0.9004 (mt) REVERT: B 622 VAL cc_start: 0.9333 (t) cc_final: 0.9119 (t) REVERT: B 623 LEU cc_start: 0.9279 (tp) cc_final: 0.8487 (tp) REVERT: B 640 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8399 (pp30) REVERT: B 647 LEU cc_start: 0.9169 (tp) cc_final: 0.8956 (tp) REVERT: C 227 GLU cc_start: 0.9242 (mp0) cc_final: 0.9009 (mp0) REVERT: C 288 GLU cc_start: 0.8117 (tp30) cc_final: 0.7503 (mm-30) REVERT: C 379 MET cc_start: 0.8947 (pmm) cc_final: 0.8660 (pmm) REVERT: C 410 MET cc_start: 0.9412 (mmt) cc_final: 0.9185 (mmp) REVERT: C 510 MET cc_start: 0.9302 (ppp) cc_final: 0.9060 (ppp) REVERT: C 540 LYS cc_start: 0.9456 (pptt) cc_final: 0.9133 (pptt) REVERT: C 730 MET cc_start: 0.9210 (mmp) cc_final: 0.8921 (mmp) REVERT: D 201 MET cc_start: 0.8962 (mtp) cc_final: 0.8623 (mtp) REVERT: D 244 ASP cc_start: 0.8671 (m-30) cc_final: 0.8375 (m-30) REVERT: D 303 ASP cc_start: 0.8184 (p0) cc_final: 0.7887 (p0) REVERT: D 379 MET cc_start: 0.9424 (mpp) cc_final: 0.9147 (mpp) REVERT: D 582 MET cc_start: 0.9204 (mmm) cc_final: 0.8734 (mmm) REVERT: D 656 ASP cc_start: 0.8941 (p0) cc_final: 0.8719 (p0) REVERT: E 183 MET cc_start: 0.9300 (ptp) cc_final: 0.8670 (ptp) REVERT: E 215 ILE cc_start: 0.9172 (mp) cc_final: 0.8608 (tp) REVERT: E 342 PHE cc_start: 0.9085 (m-10) cc_final: 0.8737 (m-80) REVERT: E 582 MET cc_start: 0.9553 (mmp) cc_final: 0.9237 (mmm) REVERT: E 594 LEU cc_start: 0.8995 (tp) cc_final: 0.8568 (tt) REVERT: E 616 ARG cc_start: 0.9100 (ptm160) cc_final: 0.8363 (tmm-80) REVERT: E 623 LEU cc_start: 0.9744 (tt) cc_final: 0.9297 (tt) REVERT: E 656 ASP cc_start: 0.9480 (p0) cc_final: 0.9102 (p0) REVERT: E 747 MET cc_start: 0.8900 (mtt) cc_final: 0.8441 (mmm) REVERT: F 201 MET cc_start: 0.9004 (mpp) cc_final: 0.8553 (mpp) REVERT: F 284 LEU cc_start: 0.9225 (tp) cc_final: 0.8979 (tp) REVERT: F 410 MET cc_start: 0.9052 (mmp) cc_final: 0.8733 (mmt) REVERT: F 510 MET cc_start: 0.9084 (tmm) cc_final: 0.8432 (tmm) REVERT: F 551 PHE cc_start: 0.9405 (m-80) cc_final: 0.9068 (m-80) REVERT: F 582 MET cc_start: 0.7441 (mpp) cc_final: 0.7087 (mpp) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.3923 time to fit residues: 183.0467 Evaluate side-chains 213 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 209 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053280 restraints weight = 163171.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054825 restraints weight = 101658.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055938 restraints weight = 71564.530| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.140 Angle : 0.612 9.272 37207 Z= 0.297 Chirality : 0.042 0.166 4245 Planarity : 0.004 0.056 4825 Dihedral : 8.386 175.183 3835 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3348 helix: 0.69 (0.12), residues: 1817 sheet: -0.15 (0.24), residues: 449 loop : 0.72 (0.22), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 491 HIS 0.008 0.001 HIS D 290 PHE 0.040 0.001 PHE C 791 TYR 0.020 0.001 TYR D 331 ARG 0.005 0.000 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 1309) hydrogen bonds : angle 4.92117 ( 3840) covalent geometry : bond 0.00295 (27578) covalent geometry : angle 0.61152 (37207) *********************** 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 282 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9318 (t-170) cc_final: 0.8974 (t-170) REVERT: A 379 MET cc_start: 0.9364 (mpp) cc_final: 0.8741 (mpp) REVERT: A 389 TYR cc_start: 0.8029 (m-10) cc_final: 0.7610 (m-10) REVERT: B 287 ASP cc_start: 0.9446 (m-30) cc_final: 0.9180 (m-30) REVERT: B 288 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7798 (mm-30) REVERT: B 335 ASP cc_start: 0.9113 (t70) cc_final: 0.8696 (t0) REVERT: B 338 LEU cc_start: 0.9478 (mt) cc_final: 0.8925 (mt) REVERT: B 582 MET cc_start: 0.7998 (mmp) cc_final: 0.7660 (mmm) REVERT: B 623 LEU cc_start: 0.9097 (tp) cc_final: 0.8886 (tp) REVERT: C 227 GLU cc_start: 0.9173 (mp0) cc_final: 0.8881 (mp0) REVERT: C 287 ASP cc_start: 0.8784 (t0) cc_final: 0.8379 (p0) REVERT: C 288 GLU cc_start: 0.8130 (tp30) cc_final: 0.7458 (mm-30) REVERT: C 290 HIS cc_start: 0.8357 (p90) cc_final: 0.7885 (p90) REVERT: C 379 MET cc_start: 0.9091 (pmm) cc_final: 0.8816 (pmm) REVERT: C 540 LYS cc_start: 0.9475 (pptt) cc_final: 0.9105 (pptt) REVERT: C 730 MET cc_start: 0.9180 (mmp) cc_final: 0.8907 (mmp) REVERT: D 201 MET cc_start: 0.8961 (mtp) cc_final: 0.8623 (mtm) REVERT: D 244 ASP cc_start: 0.8712 (m-30) cc_final: 0.8427 (m-30) REVERT: D 303 ASP cc_start: 0.8180 (p0) cc_final: 0.7869 (p0) REVERT: D 379 MET cc_start: 0.9418 (mpp) cc_final: 0.9139 (mpp) REVERT: D 392 ASP cc_start: 0.7929 (t0) cc_final: 0.7616 (t0) REVERT: D 582 MET cc_start: 0.9268 (mmm) cc_final: 0.8820 (mmm) REVERT: D 656 ASP cc_start: 0.8959 (p0) cc_final: 0.8742 (p0) REVERT: E 215 ILE cc_start: 0.8816 (mp) cc_final: 0.8301 (tp) REVERT: E 329 ARG cc_start: 0.9137 (mtm110) cc_final: 0.8776 (mmm160) REVERT: E 342 PHE cc_start: 0.9064 (m-10) cc_final: 0.8575 (m-80) REVERT: E 582 MET cc_start: 0.9572 (mmp) cc_final: 0.9293 (mmm) REVERT: E 594 LEU cc_start: 0.9115 (tp) cc_final: 0.8715 (tt) REVERT: E 616 ARG cc_start: 0.9136 (ptm160) cc_final: 0.8365 (tmm-80) REVERT: E 623 LEU cc_start: 0.9752 (tt) cc_final: 0.9308 (tt) REVERT: E 747 MET cc_start: 0.8996 (mtt) cc_final: 0.8483 (mmm) REVERT: F 183 MET cc_start: 0.8627 (mmp) cc_final: 0.8414 (mmp) REVERT: F 201 MET cc_start: 0.9006 (mpp) cc_final: 0.8530 (mpp) REVERT: F 331 TYR cc_start: 0.8746 (m-80) cc_final: 0.8208 (m-80) REVERT: F 379 MET cc_start: 0.9123 (mtm) cc_final: 0.8837 (ppp) REVERT: F 410 MET cc_start: 0.9157 (mmp) cc_final: 0.8852 (mmt) REVERT: F 510 MET cc_start: 0.9053 (tmm) cc_final: 0.8418 (tmm) REVERT: F 551 PHE cc_start: 0.9415 (m-80) cc_final: 0.9099 (m-80) REVERT: F 582 MET cc_start: 0.7625 (mpp) cc_final: 0.7253 (mpp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3612 time to fit residues: 165.3253 Evaluate side-chains 215 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 92 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS E 720 HIS F 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052916 restraints weight = 163939.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054487 restraints weight = 102330.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055599 restraints weight = 71709.097| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.128 Angle : 0.611 8.141 37207 Z= 0.295 Chirality : 0.042 0.237 4245 Planarity : 0.004 0.055 4825 Dihedral : 8.149 165.783 3835 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3348 helix: 0.73 (0.12), residues: 1816 sheet: -0.14 (0.24), residues: 437 loop : 0.75 (0.22), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 491 HIS 0.003 0.001 HIS A 704 PHE 0.033 0.001 PHE C 791 TYR 0.019 0.001 TYR A 331 ARG 0.009 0.000 ARG C 534 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 1309) hydrogen bonds : angle 4.86566 ( 3840) covalent geometry : bond 0.00273 (27578) covalent geometry : angle 0.61111 (37207) *********************** 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 283 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9232 (t-170) cc_final: 0.8947 (t-170) REVERT: A 379 MET cc_start: 0.9369 (mpp) cc_final: 0.8742 (mpp) REVERT: A 389 TYR cc_start: 0.8039 (m-10) cc_final: 0.7587 (m-10) REVERT: B 288 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 335 ASP cc_start: 0.9080 (t70) cc_final: 0.8656 (t0) REVERT: B 338 LEU cc_start: 0.9469 (mt) cc_final: 0.8907 (mt) REVERT: B 582 MET cc_start: 0.8061 (mmp) cc_final: 0.7770 (mmm) REVERT: C 227 GLU cc_start: 0.9315 (mp0) cc_final: 0.9067 (mp0) REVERT: C 287 ASP cc_start: 0.8791 (t0) cc_final: 0.8351 (p0) REVERT: C 288 GLU cc_start: 0.8162 (tp30) cc_final: 0.7504 (mm-30) REVERT: C 379 MET cc_start: 0.9032 (pmm) cc_final: 0.8805 (pmm) REVERT: C 410 MET cc_start: 0.9302 (mmp) cc_final: 0.8885 (mmt) REVERT: C 540 LYS cc_start: 0.9451 (pptt) cc_final: 0.9113 (pptt) REVERT: C 635 TYR cc_start: 0.8490 (m-80) cc_final: 0.8096 (m-80) REVERT: C 693 MET cc_start: 0.8116 (pmm) cc_final: 0.7881 (pmm) REVERT: C 730 MET cc_start: 0.9185 (mmp) cc_final: 0.8950 (mmp) REVERT: D 201 MET cc_start: 0.8997 (mtp) cc_final: 0.8624 (mtm) REVERT: D 244 ASP cc_start: 0.8701 (m-30) cc_final: 0.8410 (m-30) REVERT: D 303 ASP cc_start: 0.8158 (p0) cc_final: 0.7859 (p0) REVERT: D 379 MET cc_start: 0.9432 (mpp) cc_final: 0.9175 (mpp) REVERT: D 392 ASP cc_start: 0.7986 (t0) cc_final: 0.7620 (t0) REVERT: D 582 MET cc_start: 0.9201 (mmm) cc_final: 0.8817 (mmm) REVERT: D 656 ASP cc_start: 0.8970 (p0) cc_final: 0.8732 (p0) REVERT: E 215 ILE cc_start: 0.8807 (mp) cc_final: 0.8303 (tp) REVERT: E 329 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8778 (mmm160) REVERT: E 342 PHE cc_start: 0.9070 (m-10) cc_final: 0.8562 (m-80) REVERT: E 582 MET cc_start: 0.9525 (mmp) cc_final: 0.9323 (mmm) REVERT: E 594 LEU cc_start: 0.9146 (tp) cc_final: 0.8734 (tp) REVERT: E 616 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8325 (tmm-80) REVERT: E 623 LEU cc_start: 0.9745 (tt) cc_final: 0.9399 (tt) REVERT: E 693 MET cc_start: 0.8466 (pmm) cc_final: 0.8259 (pmm) REVERT: E 747 MET cc_start: 0.8987 (mtt) cc_final: 0.8488 (mmm) REVERT: F 201 MET cc_start: 0.8975 (mpp) cc_final: 0.8485 (mpp) REVERT: F 284 LEU cc_start: 0.9267 (tp) cc_final: 0.9060 (tp) REVERT: F 330 LYS cc_start: 0.9149 (ptmm) cc_final: 0.8909 (ptmt) REVERT: F 331 TYR cc_start: 0.8795 (m-80) cc_final: 0.7953 (m-80) REVERT: F 379 MET cc_start: 0.9097 (mtm) cc_final: 0.8796 (ppp) REVERT: F 410 MET cc_start: 0.9143 (mmp) cc_final: 0.8848 (mmt) REVERT: F 510 MET cc_start: 0.9086 (tmm) cc_final: 0.8432 (tmm) REVERT: F 551 PHE cc_start: 0.9421 (m-80) cc_final: 0.9108 (m-80) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3837 time to fit residues: 174.1610 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 : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 288 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 333 optimal weight: 0.0270 chunk 5 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 229 optimal weight: 0.0170 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052049 restraints weight = 163087.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053605 restraints weight = 101633.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054697 restraints weight = 71114.492| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27578 Z= 0.152 Angle : 0.626 7.741 37207 Z= 0.305 Chirality : 0.042 0.300 4245 Planarity : 0.004 0.055 4825 Dihedral : 7.871 154.977 3835 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3348 helix: 0.74 (0.12), residues: 1814 sheet: -0.18 (0.24), residues: 445 loop : 0.77 (0.22), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 491 HIS 0.004 0.001 HIS D 515 PHE 0.033 0.001 PHE C 791 TYR 0.021 0.001 TYR D 331 ARG 0.006 0.000 ARG C 534 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 1309) hydrogen bonds : angle 4.90890 ( 3840) covalent geometry : bond 0.00322 (27578) covalent geometry : angle 0.62637 (37207) *********************** 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 274 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 2.938 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 354 HIS cc_start: 0.9261 (t-170) cc_final: 0.8996 (t-170) REVERT: A 379 MET cc_start: 0.9380 (mpp) cc_final: 0.8732 (mpp) REVERT: A 389 TYR cc_start: 0.8073 (m-10) cc_final: 0.7592 (m-10) REVERT: A 625 ASP cc_start: 0.8309 (t70) cc_final: 0.8037 (t70) REVERT: B 287 ASP cc_start: 0.9557 (m-30) cc_final: 0.9346 (m-30) REVERT: B 288 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 290 HIS cc_start: 0.9328 (p90) cc_final: 0.8846 (p90) REVERT: B 338 LEU cc_start: 0.9478 (mt) cc_final: 0.9244 (mt) REVERT: B 379 MET cc_start: 0.9014 (pmm) cc_final: 0.8708 (pmm) REVERT: B 582 MET cc_start: 0.8076 (mmp) cc_final: 0.7797 (mmm) REVERT: B 623 LEU cc_start: 0.9100 (tp) cc_final: 0.8891 (tp) REVERT: C 287 ASP cc_start: 0.8722 (t0) cc_final: 0.8316 (p0) REVERT: C 288 GLU cc_start: 0.8284 (tp30) cc_final: 0.7596 (mm-30) REVERT: C 290 HIS cc_start: 0.8505 (p90) cc_final: 0.7975 (p90) REVERT: C 379 MET cc_start: 0.9007 (pmm) cc_final: 0.8743 (pmm) REVERT: C 540 LYS cc_start: 0.9454 (pptt) cc_final: 0.9133 (pptt) REVERT: C 635 TYR cc_start: 0.8388 (m-80) cc_final: 0.7931 (m-80) REVERT: C 730 MET cc_start: 0.9192 (mmp) cc_final: 0.8960 (mmp) REVERT: D 201 MET cc_start: 0.8998 (mtp) cc_final: 0.8637 (mtm) REVERT: D 244 ASP cc_start: 0.8737 (m-30) cc_final: 0.8450 (m-30) REVERT: D 379 MET cc_start: 0.9458 (mpp) cc_final: 0.8466 (mpp) REVERT: D 392 ASP cc_start: 0.8042 (t0) cc_final: 0.7658 (t0) REVERT: D 582 MET cc_start: 0.9208 (mmm) cc_final: 0.8828 (mmm) REVERT: D 656 ASP cc_start: 0.8937 (p0) cc_final: 0.8709 (p0) REVERT: E 215 ILE cc_start: 0.8796 (mp) cc_final: 0.8181 (tp) REVERT: E 329 ARG cc_start: 0.9158 (mtm110) cc_final: 0.8778 (mmm160) REVERT: E 342 PHE cc_start: 0.9033 (m-10) cc_final: 0.8484 (m-80) REVERT: E 582 MET cc_start: 0.9534 (mmp) cc_final: 0.9318 (mmm) REVERT: E 594 LEU cc_start: 0.9176 (tp) cc_final: 0.8759 (tp) REVERT: E 616 ARG cc_start: 0.9148 (ptm160) cc_final: 0.8356 (tmm-80) REVERT: E 623 LEU cc_start: 0.9763 (tt) cc_final: 0.9409 (tt) REVERT: E 693 MET cc_start: 0.8220 (pmm) cc_final: 0.8004 (pmm) REVERT: F 201 MET cc_start: 0.9022 (mpp) cc_final: 0.8507 (mpp) REVERT: F 284 LEU cc_start: 0.9265 (tp) cc_final: 0.9025 (tp) REVERT: F 330 LYS cc_start: 0.9174 (ptmm) cc_final: 0.8817 (ptmm) REVERT: F 331 TYR cc_start: 0.8811 (m-80) cc_final: 0.8086 (m-80) REVERT: F 379 MET cc_start: 0.9076 (mtm) cc_final: 0.8781 (ppp) REVERT: F 510 MET cc_start: 0.9145 (tmm) cc_final: 0.8686 (tmm) REVERT: F 551 PHE cc_start: 0.9438 (m-80) cc_final: 0.9202 (m-80) REVERT: F 582 MET cc_start: 0.7220 (mpp) cc_final: 0.6916 (mpp) REVERT: F 734 MET cc_start: 0.9108 (mpp) cc_final: 0.8675 (mpp) REVERT: F 747 MET cc_start: 0.8095 (tpt) cc_final: 0.7590 (mmm) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.3646 time to fit residues: 160.7718 Evaluate side-chains 208 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 97 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3390 r_free = 0.3390 target = 0.065217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051998 restraints weight = 163911.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053539 restraints weight = 101622.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054623 restraints weight = 71191.561| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.142 Angle : 0.630 8.384 37207 Z= 0.306 Chirality : 0.043 0.239 4245 Planarity : 0.004 0.099 4825 Dihedral : 7.765 149.139 3835 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3348 helix: 0.72 (0.12), residues: 1827 sheet: -0.23 (0.24), residues: 429 loop : 0.74 (0.22), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 491 HIS 0.003 0.001 HIS D 515 PHE 0.033 0.001 PHE F 497 TYR 0.022 0.002 TYR D 331 ARG 0.007 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 1309) hydrogen bonds : angle 4.88243 ( 3840) covalent geometry : bond 0.00302 (27578) covalent geometry : angle 0.62953 (37207) *********************** 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 279 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 3.140 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 328 TYR cc_start: 0.9176 (t80) cc_final: 0.8956 (t80) REVERT: A 330 LYS cc_start: 0.9379 (tmmt) cc_final: 0.8872 (tmmt) REVERT: A 354 HIS cc_start: 0.9350 (t-170) cc_final: 0.8975 (t-170) REVERT: A 379 MET cc_start: 0.9386 (mpp) cc_final: 0.8721 (mpp) REVERT: A 389 TYR cc_start: 0.8047 (m-10) cc_final: 0.7580 (m-10) REVERT: A 625 ASP cc_start: 0.8278 (t70) cc_final: 0.8066 (t70) REVERT: B 251 ASP cc_start: 0.8826 (t70) cc_final: 0.8601 (t0) REVERT: B 287 ASP cc_start: 0.9556 (m-30) cc_final: 0.9354 (m-30) REVERT: B 288 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 338 LEU cc_start: 0.9466 (mt) cc_final: 0.9241 (mt) REVERT: B 582 MET cc_start: 0.8114 (mmp) cc_final: 0.7806 (mmm) REVERT: B 623 LEU cc_start: 0.9091 (tp) cc_final: 0.8851 (tp) REVERT: C 287 ASP cc_start: 0.8719 (t0) cc_final: 0.8303 (p0) REVERT: C 288 GLU cc_start: 0.8273 (tp30) cc_final: 0.7678 (mm-30) REVERT: C 290 HIS cc_start: 0.8501 (p90) cc_final: 0.8010 (p90) REVERT: C 379 MET cc_start: 0.8951 (pmm) cc_final: 0.8630 (pmm) REVERT: C 410 MET cc_start: 0.9262 (mmp) cc_final: 0.8964 (mmt) REVERT: C 540 LYS cc_start: 0.9470 (pptt) cc_final: 0.9151 (pptt) REVERT: C 635 TYR cc_start: 0.8145 (m-80) cc_final: 0.7670 (m-80) REVERT: C 730 MET cc_start: 0.9192 (mmp) cc_final: 0.8959 (mmp) REVERT: D 201 MET cc_start: 0.9030 (mtp) cc_final: 0.8669 (mtm) REVERT: D 244 ASP cc_start: 0.8757 (m-30) cc_final: 0.8456 (m-30) REVERT: D 379 MET cc_start: 0.9437 (mpp) cc_final: 0.8502 (mpp) REVERT: D 582 MET cc_start: 0.9168 (mmm) cc_final: 0.8800 (mmm) REVERT: D 656 ASP cc_start: 0.8949 (p0) cc_final: 0.8728 (p0) REVERT: E 215 ILE cc_start: 0.8798 (mp) cc_final: 0.8119 (tp) REVERT: E 342 PHE cc_start: 0.9012 (m-10) cc_final: 0.8565 (m-80) REVERT: E 582 MET cc_start: 0.9531 (mmp) cc_final: 0.9311 (mmm) REVERT: E 594 LEU cc_start: 0.9199 (tp) cc_final: 0.8780 (tp) REVERT: E 616 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8351 (tmm-80) REVERT: E 623 LEU cc_start: 0.9764 (tt) cc_final: 0.9390 (tt) REVERT: E 693 MET cc_start: 0.8215 (pmm) cc_final: 0.7984 (pmm) REVERT: F 201 MET cc_start: 0.8996 (mpp) cc_final: 0.8554 (mpp) REVERT: F 284 LEU cc_start: 0.9260 (tp) cc_final: 0.9012 (tp) REVERT: F 331 TYR cc_start: 0.8760 (m-80) cc_final: 0.8180 (m-80) REVERT: F 379 MET cc_start: 0.9061 (mtm) cc_final: 0.8762 (ppp) REVERT: F 510 MET cc_start: 0.9123 (tmm) cc_final: 0.8643 (tmm) REVERT: F 551 PHE cc_start: 0.9445 (m-80) cc_final: 0.9207 (m-80) REVERT: F 582 MET cc_start: 0.7250 (mpp) cc_final: 0.6928 (mpp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3805 time to fit residues: 170.1132 Evaluate side-chains 213 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 609 GLN ** 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051798 restraints weight = 162671.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053338 restraints weight = 101212.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054457 restraints weight = 70685.295| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.154 Angle : 0.647 10.067 37207 Z= 0.316 Chirality : 0.043 0.228 4245 Planarity : 0.004 0.062 4825 Dihedral : 7.709 148.393 3835 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1821 sheet: -0.26 (0.24), residues: 443 loop : 0.76 (0.22), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 491 HIS 0.004 0.001 HIS C 631 PHE 0.031 0.001 PHE C 791 TYR 0.023 0.002 TYR D 331 ARG 0.008 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 1309) hydrogen bonds : angle 4.94661 ( 3840) covalent geometry : bond 0.00329 (27578) covalent geometry : angle 0.64740 (37207) *********************** 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 277 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.894 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: A 330 LYS cc_start: 0.9405 (tmmt) cc_final: 0.8912 (tmmt) REVERT: A 354 HIS cc_start: 0.9298 (t-170) cc_final: 0.8976 (t-170) REVERT: A 389 TYR cc_start: 0.8079 (m-10) cc_final: 0.7604 (m-10) REVERT: A 625 ASP cc_start: 0.8263 (t70) cc_final: 0.8036 (t70) REVERT: B 251 ASP cc_start: 0.8872 (t70) cc_final: 0.8616 (t0) REVERT: B 338 LEU cc_start: 0.9477 (mt) cc_final: 0.9250 (mt) REVERT: B 379 MET cc_start: 0.8878 (pmm) cc_final: 0.8633 (pmm) REVERT: B 582 MET cc_start: 0.8099 (mmp) cc_final: 0.7680 (mmm) REVERT: B 623 LEU cc_start: 0.9117 (tp) cc_final: 0.8887 (tp) REVERT: B 693 MET cc_start: 0.7892 (pmm) cc_final: 0.7690 (pmm) REVERT: C 227 GLU cc_start: 0.9500 (mp0) cc_final: 0.9194 (mp0) REVERT: C 287 ASP cc_start: 0.8722 (t0) cc_final: 0.8325 (p0) REVERT: C 288 GLU cc_start: 0.8291 (tp30) cc_final: 0.7747 (mm-30) REVERT: C 290 HIS cc_start: 0.8552 (p90) cc_final: 0.8042 (p90) REVERT: C 379 MET cc_start: 0.9034 (pmm) cc_final: 0.8633 (pmm) REVERT: C 410 MET cc_start: 0.9288 (mmp) cc_final: 0.8992 (mmt) REVERT: C 510 MET cc_start: 0.9322 (ppp) cc_final: 0.9115 (ppp) REVERT: C 540 LYS cc_start: 0.9488 (pptt) cc_final: 0.9166 (pptt) REVERT: C 616 ARG cc_start: 0.8973 (mpt180) cc_final: 0.8185 (mmt-90) REVERT: C 635 TYR cc_start: 0.8172 (m-80) cc_final: 0.7761 (m-80) REVERT: C 730 MET cc_start: 0.9196 (mmp) cc_final: 0.8960 (mmp) REVERT: D 201 MET cc_start: 0.9039 (mtp) cc_final: 0.8680 (mtm) REVERT: D 244 ASP cc_start: 0.8770 (m-30) cc_final: 0.8465 (m-30) REVERT: D 379 MET cc_start: 0.9449 (mpp) cc_final: 0.8771 (mpp) REVERT: D 582 MET cc_start: 0.9189 (mmm) cc_final: 0.8797 (mmm) REVERT: D 656 ASP cc_start: 0.8784 (p0) cc_final: 0.8524 (p0) REVERT: E 215 ILE cc_start: 0.8908 (mp) cc_final: 0.8200 (tp) REVERT: E 342 PHE cc_start: 0.8989 (m-10) cc_final: 0.8542 (m-80) REVERT: E 582 MET cc_start: 0.9553 (mmp) cc_final: 0.9251 (mmm) REVERT: E 616 ARG cc_start: 0.9134 (ptm160) cc_final: 0.8353 (tmm-80) REVERT: E 623 LEU cc_start: 0.9783 (tt) cc_final: 0.9312 (tt) REVERT: E 693 MET cc_start: 0.8200 (pmm) cc_final: 0.7968 (pmm) REVERT: E 747 MET cc_start: 0.8371 (mmt) cc_final: 0.7837 (mmm) REVERT: F 201 MET cc_start: 0.8995 (mpp) cc_final: 0.8544 (mpp) REVERT: F 284 LEU cc_start: 0.9269 (tp) cc_final: 0.9016 (tp) REVERT: F 330 LYS cc_start: 0.9179 (ptmt) cc_final: 0.8899 (ptmm) REVERT: F 331 TYR cc_start: 0.8758 (m-80) cc_final: 0.8252 (m-80) REVERT: F 379 MET cc_start: 0.9033 (mtm) cc_final: 0.8754 (ppp) REVERT: F 510 MET cc_start: 0.9206 (tmm) cc_final: 0.8699 (tmm) REVERT: F 551 PHE cc_start: 0.9357 (m-80) cc_final: 0.9103 (m-80) REVERT: F 582 MET cc_start: 0.7321 (mpp) cc_final: 0.6827 (mpp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3646 time to fit residues: 162.4641 Evaluate side-chains 213 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 66 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 202 GLN E 290 HIS E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052095 restraints weight = 161178.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053641 restraints weight = 100324.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054758 restraints weight = 70230.202| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.139 Angle : 0.648 9.623 37207 Z= 0.315 Chirality : 0.043 0.218 4245 Planarity : 0.004 0.054 4825 Dihedral : 7.624 147.707 3835 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1822 sheet: -0.26 (0.24), residues: 442 loop : 0.77 (0.22), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 491 HIS 0.005 0.001 HIS E 354 PHE 0.050 0.001 PHE F 497 TYR 0.026 0.002 TYR C 604 ARG 0.013 0.000 ARG F 653 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 1309) hydrogen bonds : angle 4.92040 ( 3840) covalent geometry : bond 0.00299 (27578) covalent geometry : angle 0.64771 (37207) ********************** 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 271 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9766 (mp) cc_final: 0.9564 (mp) REVERT: A 330 LYS cc_start: 0.9439 (tmmt) cc_final: 0.8983 (tmmt) REVERT: A 354 HIS cc_start: 0.9363 (t-170) cc_final: 0.8961 (t-170) REVERT: A 389 TYR cc_start: 0.8112 (m-10) cc_final: 0.7622 (m-10) REVERT: A 625 ASP cc_start: 0.8258 (t70) cc_final: 0.7991 (t70) REVERT: B 251 ASP cc_start: 0.8858 (t70) cc_final: 0.8601 (t0) REVERT: B 338 LEU cc_start: 0.9471 (mt) cc_final: 0.9243 (mt) REVERT: B 379 MET cc_start: 0.8792 (pmm) cc_final: 0.8545 (pmm) REVERT: B 582 MET cc_start: 0.8080 (mmp) cc_final: 0.7679 (mmm) REVERT: C 227 GLU cc_start: 0.9497 (mp0) cc_final: 0.9204 (mp0) REVERT: C 271 LYS cc_start: 0.9573 (tptp) cc_final: 0.9317 (tptp) REVERT: C 287 ASP cc_start: 0.8695 (t0) cc_final: 0.8314 (p0) REVERT: C 288 GLU cc_start: 0.8288 (tp30) cc_final: 0.7761 (mm-30) REVERT: C 290 HIS cc_start: 0.8534 (p90) cc_final: 0.8073 (p90) REVERT: C 379 MET cc_start: 0.9026 (pmm) cc_final: 0.8614 (pmm) REVERT: C 410 MET cc_start: 0.9286 (mmp) cc_final: 0.8999 (mmt) REVERT: C 510 MET cc_start: 0.9318 (ppp) cc_final: 0.9101 (ppp) REVERT: C 540 LYS cc_start: 0.9484 (pptt) cc_final: 0.9157 (pptt) REVERT: C 635 TYR cc_start: 0.8140 (m-80) cc_final: 0.7766 (m-80) REVERT: C 693 MET cc_start: 0.8223 (pmm) cc_final: 0.7974 (pmm) REVERT: C 730 MET cc_start: 0.9189 (mmp) cc_final: 0.8964 (mmp) REVERT: D 201 MET cc_start: 0.9045 (mtp) cc_final: 0.8706 (mtp) REVERT: D 244 ASP cc_start: 0.8758 (m-30) cc_final: 0.8450 (m-30) REVERT: D 379 MET cc_start: 0.9433 (mpp) cc_final: 0.8777 (mpp) REVERT: D 582 MET cc_start: 0.9177 (mmm) cc_final: 0.8811 (mmm) REVERT: D 656 ASP cc_start: 0.8757 (p0) cc_final: 0.8535 (p0) REVERT: E 215 ILE cc_start: 0.8884 (mp) cc_final: 0.8130 (tp) REVERT: E 342 PHE cc_start: 0.8975 (m-10) cc_final: 0.8524 (m-80) REVERT: E 582 MET cc_start: 0.9541 (mmp) cc_final: 0.9259 (mmm) REVERT: E 616 ARG cc_start: 0.9130 (ptm160) cc_final: 0.8397 (tmm-80) REVERT: E 623 LEU cc_start: 0.9779 (tt) cc_final: 0.9310 (tt) REVERT: E 693 MET cc_start: 0.8173 (pmm) cc_final: 0.7931 (pmm) REVERT: E 747 MET cc_start: 0.8456 (mmt) cc_final: 0.7800 (mmm) REVERT: F 201 MET cc_start: 0.9002 (mpp) cc_final: 0.8430 (mpp) REVERT: F 284 LEU cc_start: 0.9247 (tp) cc_final: 0.8995 (tp) REVERT: F 330 LYS cc_start: 0.9182 (ptmt) cc_final: 0.8889 (ptmm) REVERT: F 331 TYR cc_start: 0.8768 (m-80) cc_final: 0.8254 (m-80) REVERT: F 379 MET cc_start: 0.9010 (mtm) cc_final: 0.8733 (ppp) REVERT: F 510 MET cc_start: 0.9199 (tmm) cc_final: 0.8695 (tmm) REVERT: F 551 PHE cc_start: 0.9353 (m-80) cc_final: 0.9095 (m-80) REVERT: F 582 MET cc_start: 0.7252 (mpp) cc_final: 0.6802 (mpp) REVERT: F 730 MET cc_start: 0.8413 (mmp) cc_final: 0.7941 (mmt) REVERT: F 734 MET cc_start: 0.9213 (mpp) cc_final: 0.8945 (mmm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3668 time to fit residues: 161.2445 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 : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 107 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 317 optimal weight: 0.2980 chunk 247 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3396 r_free = 0.3396 target = 0.065504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052417 restraints weight = 160925.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053972 restraints weight = 99935.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055071 restraints weight = 69859.922| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27578 Z= 0.118 Angle : 0.638 9.697 37207 Z= 0.308 Chirality : 0.043 0.214 4245 Planarity : 0.004 0.053 4825 Dihedral : 7.513 146.939 3835 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3348 helix: 0.74 (0.12), residues: 1822 sheet: -0.20 (0.24), residues: 434 loop : 0.80 (0.22), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 491 HIS 0.002 0.001 HIS C 369 PHE 0.030 0.001 PHE C 791 TYR 0.020 0.002 TYR D 331 ARG 0.007 0.000 ARG F 653 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 1309) hydrogen bonds : angle 4.86236 ( 3840) covalent geometry : bond 0.00258 (27578) covalent geometry : angle 0.63828 (37207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7395.96 seconds wall clock time: 130 minutes 59.81 seconds (7859.81 seconds total)