Starting phenix.real_space_refine on Mon Jun 23 18:42:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8w_15242/06_2025/8a8w_15242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8w_15242/06_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_15242/06_2025/8a8w_15242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8w_15242/06_2025/8a8w_15242.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8w_15242/06_2025/8a8w_15242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8w_15242/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.40, per 1000 atoms: 0.68 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: 7.65 Conformation dependent library (CDL) restraints added in 3.9 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: 3.31 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: 11.56 Time building geometry restraints manager: 8.77 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 67.260 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.470 ------------------------------------------------------------------------------- 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 : 3.189 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: 0.6939 (tp30) REVERT: C 410 MET cc_start: 0.9329 (mmt) cc_final: 0.9111 (mmp) REVERT: C 579 GLN cc_start: 0.8253 (tm130) cc_final: 0.7996 (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: 0.8846 (m-30) REVERT: D 582 MET cc_start: 0.9029 (mmm) cc_final: 0.8578 (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: 0.3843 time to fit residues: 207.6886 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 : 3.122 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.069584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055896 restraints weight = 155736.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057586 restraints weight = 95829.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058797 restraints weight = 66842.974| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27578 Z= 0.107 Angle : 0.611 7.829 37207 Z= 0.296 Chirality : 0.042 0.192 4245 Planarity : 0.004 0.068 4825 Dihedral : 8.848 173.829 3835 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.30 (0.15), residues: 3348 helix: 0.38 (0.12), residues: 1806 sheet: -0.06 (0.25), residues: 419 loop : 0.32 (0.20), residues: 1123 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 0.032 0.001 PHE F 497 TYR 0.019 0.001 TYR A 331 ARG 0.005 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 1309) hydrogen bonds : angle 5.21753 ( 3840) covalent geometry : bond 0.00223 (27578) covalent geometry : angle 0.61066 (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 : 3.669 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 178 LEU cc_start: 0.9706 (mp) cc_final: 0.9435 (mp) REVERT: A 250 LEU cc_start: 0.9062 (tt) cc_final: 0.8763 (tt) REVERT: A 379 MET cc_start: 0.9292 (mpp) cc_final: 0.8720 (mpp) REVERT: A 389 TYR cc_start: 0.8036 (m-10) cc_final: 0.7819 (m-10) REVERT: A 662 LEU cc_start: 0.9417 (mt) cc_final: 0.9156 (mt) REVERT: B 287 ASP cc_start: 0.9401 (m-30) cc_final: 0.9140 (m-30) REVERT: B 335 ASP cc_start: 0.9353 (t70) cc_final: 0.9007 (t0) REVERT: B 338 LEU cc_start: 0.9386 (mt) cc_final: 0.8930 (mt) REVERT: B 622 VAL cc_start: 0.9114 (t) cc_final: 0.8817 (t) REVERT: C 227 GLU cc_start: 0.9350 (mp0) cc_final: 0.9103 (mp0) REVERT: C 379 MET cc_start: 0.9148 (pmm) cc_final: 0.8900 (pmm) REVERT: C 410 MET cc_start: 0.9417 (mmt) cc_final: 0.9197 (mmp) REVERT: C 579 GLN cc_start: 0.7965 (tm130) cc_final: 0.7745 (tm-30) REVERT: C 693 MET cc_start: 0.8240 (pmm) cc_final: 0.7995 (pmm) REVERT: C 730 MET cc_start: 0.9214 (mmp) cc_final: 0.8898 (mmp) REVERT: D 201 MET cc_start: 0.9028 (mtp) cc_final: 0.8565 (mtm) REVERT: D 233 ILE cc_start: 0.9393 (mt) cc_final: 0.9132 (tt) REVERT: D 244 ASP cc_start: 0.8652 (m-30) cc_final: 0.8315 (m-30) REVERT: D 303 ASP cc_start: 0.7852 (p0) cc_final: 0.7456 (p0) REVERT: D 346 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8632 (mm-40) REVERT: D 379 MET cc_start: 0.9273 (mpp) cc_final: 0.8653 (mpp) REVERT: D 582 MET cc_start: 0.8862 (mmm) cc_final: 0.8554 (mmm) REVERT: D 627 ILE cc_start: 0.9478 (tp) cc_final: 0.9271 (tp) REVERT: D 638 LEU cc_start: 0.9457 (mp) cc_final: 0.9252 (mp) REVERT: D 656 ASP cc_start: 0.9014 (p0) cc_final: 0.8813 (p0) REVERT: D 710 LEU cc_start: 0.9436 (mt) cc_final: 0.9135 (mt) REVERT: D 711 ASN cc_start: 0.8898 (m-40) cc_final: 0.8239 (t0) REVERT: D 730 MET cc_start: 0.9078 (tpp) cc_final: 0.8737 (tpp) REVERT: E 183 MET cc_start: 0.9307 (ptp) cc_final: 0.8694 (ptp) REVERT: E 342 PHE cc_start: 0.9137 (m-80) cc_final: 0.8705 (m-80) REVERT: E 357 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8658 (mm-30) REVERT: E 582 MET cc_start: 0.9447 (mmp) cc_final: 0.9225 (mmm) REVERT: E 616 ARG cc_start: 0.9031 (ptm160) cc_final: 0.8172 (tmm-80) REVERT: E 623 LEU cc_start: 0.9667 (tt) cc_final: 0.9365 (tt) REVERT: E 656 ASP cc_start: 0.9507 (p0) cc_final: 0.9301 (p0) REVERT: E 709 PHE cc_start: 0.9005 (t80) cc_final: 0.8610 (t80) REVERT: F 200 VAL cc_start: 0.9422 (p) cc_final: 0.9057 (p) REVERT: F 201 MET cc_start: 0.8935 (mpp) cc_final: 0.8450 (mpp) REVERT: F 510 MET cc_start: 0.8885 (tmm) cc_final: 0.8323 (tmm) REVERT: F 551 PHE cc_start: 0.9439 (m-80) cc_final: 0.9126 (m-10) REVERT: F 582 MET cc_start: 0.7373 (mpp) cc_final: 0.7048 (mpp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.4508 time to fit residues: 237.9600 Evaluate side-chains 238 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 4.691 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 315 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 391 ASN D 370 HIS D 632 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS E 568 ASN F 290 HIS F 391 ASN F 515 HIS F 741 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052956 restraints weight = 162846.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054491 restraints weight = 101361.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055600 restraints weight = 71151.374| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27578 Z= 0.189 Angle : 0.647 8.151 37207 Z= 0.319 Chirality : 0.042 0.171 4245 Planarity : 0.004 0.064 4825 Dihedral : 8.755 179.262 3835 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % 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: 0.48 (0.15), residues: 3348 helix: 0.52 (0.12), residues: 1825 sheet: -0.20 (0.24), residues: 426 loop : 0.52 (0.21), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 491 HIS 0.007 0.001 HIS C 290 PHE 0.027 0.002 PHE C 791 TYR 0.017 0.002 TYR A 331 ARG 0.004 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1309) hydrogen bonds : angle 5.09341 ( 3840) covalent geometry : bond 0.00388 (27578) covalent geometry : angle 0.64708 (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 287 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9722 (mp) cc_final: 0.9499 (mp) REVERT: A 250 LEU cc_start: 0.9183 (tt) cc_final: 0.8888 (tt) REVERT: A 354 HIS cc_start: 0.9361 (t-170) cc_final: 0.9056 (t-170) REVERT: A 379 MET cc_start: 0.9400 (mpp) cc_final: 0.8745 (mpp) REVERT: A 389 TYR cc_start: 0.8015 (m-10) cc_final: 0.7699 (m-10) REVERT: B 287 ASP cc_start: 0.9474 (m-30) cc_final: 0.9223 (m-30) REVERT: B 335 ASP cc_start: 0.9190 (t70) cc_final: 0.8787 (t0) REVERT: B 338 LEU cc_start: 0.9527 (mt) cc_final: 0.9055 (mt) REVERT: B 622 VAL cc_start: 0.9255 (t) cc_final: 0.9008 (t) REVERT: B 623 LEU cc_start: 0.9218 (tp) cc_final: 0.8991 (tp) REVERT: C 227 GLU cc_start: 0.9230 (mp0) cc_final: 0.8958 (mp0) REVERT: C 287 ASP cc_start: 0.8611 (t0) cc_final: 0.8311 (t70) REVERT: C 379 MET cc_start: 0.8937 (pmm) cc_final: 0.8724 (pmm) REVERT: C 410 MET cc_start: 0.9410 (mmt) cc_final: 0.9197 (mmp) REVERT: C 540 LYS cc_start: 0.9517 (pptt) cc_final: 0.9204 (pptt) REVERT: C 730 MET cc_start: 0.9237 (mmp) cc_final: 0.8859 (mmp) REVERT: D 201 MET cc_start: 0.9001 (mtp) cc_final: 0.8616 (mtm) REVERT: D 288 GLU cc_start: 0.7969 (pp20) cc_final: 0.7622 (pp20) REVERT: D 303 ASP cc_start: 0.8165 (p0) cc_final: 0.7878 (p0) REVERT: D 346 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8580 (mm-40) REVERT: D 379 MET cc_start: 0.9364 (mpp) cc_final: 0.9119 (mpp) REVERT: D 582 MET cc_start: 0.9226 (mmm) cc_final: 0.8798 (mmm) REVERT: D 638 LEU cc_start: 0.9575 (mp) cc_final: 0.9370 (mp) REVERT: E 183 MET cc_start: 0.9289 (ptp) cc_final: 0.8700 (ptp) REVERT: E 215 ILE cc_start: 0.9319 (mp) cc_final: 0.8537 (tp) REVERT: E 290 HIS cc_start: 0.9111 (p-80) cc_final: 0.8831 (p90) REVERT: E 342 PHE cc_start: 0.9123 (m-80) cc_final: 0.8731 (m-80) REVERT: E 582 MET cc_start: 0.9606 (mmp) cc_final: 0.9295 (mmm) REVERT: E 594 LEU cc_start: 0.8885 (tp) cc_final: 0.8454 (tt) REVERT: E 616 ARG cc_start: 0.9097 (ptm160) cc_final: 0.8345 (tmm-80) REVERT: E 623 LEU cc_start: 0.9736 (tt) cc_final: 0.9309 (tt) REVERT: E 747 MET cc_start: 0.8981 (mtt) cc_final: 0.8560 (mmm) REVERT: F 201 MET cc_start: 0.9150 (mpp) cc_final: 0.8692 (mpp) REVERT: F 330 LYS cc_start: 0.9105 (ptmm) cc_final: 0.8852 (ptmm) REVERT: F 331 TYR cc_start: 0.8394 (m-80) cc_final: 0.7537 (m-80) REVERT: F 510 MET cc_start: 0.8998 (tmm) cc_final: 0.8454 (tmm) REVERT: F 551 PHE cc_start: 0.9433 (m-80) cc_final: 0.9219 (m-10) REVERT: F 582 MET cc_start: 0.7498 (mpp) cc_final: 0.7025 (mpp) outliers start: 2 outliers final: 0 residues processed: 287 average time/residue: 0.3636 time to fit residues: 170.2933 Evaluate side-chains 218 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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: 3.9990 chunk 184 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 0.0770 chunk 40 optimal weight: 10.0000 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS B 640 GLN C 391 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053815 restraints weight = 160785.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055444 restraints weight = 98519.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056600 restraints weight = 68623.117| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1813 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= 0.108 Angle : 0.601 7.547 37207 Z= 0.288 Chirality : 0.042 0.224 4245 Planarity : 0.004 0.059 4825 Dihedral : 8.477 179.964 3835 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % 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: 0.68 (0.15), residues: 3348 helix: 0.67 (0.12), residues: 1817 sheet: -0.16 (0.25), residues: 427 loop : 0.67 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 491 HIS 0.002 0.000 HIS E 631 PHE 0.030 0.001 PHE F 497 TYR 0.013 0.001 TYR D 331 ARG 0.006 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 1309) hydrogen bonds : angle 4.89071 ( 3840) covalent geometry : bond 0.00231 (27578) covalent geometry : angle 0.60106 (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 297 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9738 (mp) cc_final: 0.9533 (mp) REVERT: A 354 HIS cc_start: 0.9303 (t-170) cc_final: 0.8975 (t-170) REVERT: A 379 MET cc_start: 0.9416 (mpp) cc_final: 0.8736 (mpp) REVERT: A 389 TYR cc_start: 0.8002 (m-10) cc_final: 0.7595 (m-10) REVERT: B 287 ASP cc_start: 0.9337 (m-30) cc_final: 0.9070 (m-30) REVERT: B 288 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 335 ASP cc_start: 0.9183 (t70) cc_final: 0.8746 (t0) REVERT: B 338 LEU cc_start: 0.9458 (mt) cc_final: 0.9006 (mt) REVERT: B 622 VAL cc_start: 0.9322 (t) cc_final: 0.9079 (t) REVERT: B 623 LEU cc_start: 0.9214 (tp) cc_final: 0.8408 (tp) REVERT: B 640 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8304 (pp30) REVERT: B 647 LEU cc_start: 0.9154 (tp) cc_final: 0.8889 (tp) REVERT: C 227 GLU cc_start: 0.9272 (mp0) cc_final: 0.9065 (mp0) REVERT: C 271 LYS cc_start: 0.9581 (tptp) cc_final: 0.9380 (tppt) REVERT: C 290 HIS cc_start: 0.8540 (p90) cc_final: 0.8164 (p-80) REVERT: C 379 MET cc_start: 0.8974 (pmm) cc_final: 0.8670 (pmm) REVERT: C 410 MET cc_start: 0.9425 (mmt) cc_final: 0.9192 (mmp) REVERT: C 510 MET cc_start: 0.9311 (ppp) cc_final: 0.9049 (ppp) REVERT: C 540 LYS cc_start: 0.9481 (pptt) cc_final: 0.9161 (pptt) REVERT: C 646 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8366 (ptp-170) REVERT: C 730 MET cc_start: 0.9204 (mmp) cc_final: 0.8874 (mmp) REVERT: C 747 MET cc_start: 0.8277 (mtt) cc_final: 0.7945 (mtt) REVERT: D 201 MET cc_start: 0.8994 (mtp) cc_final: 0.8609 (mtm) REVERT: D 244 ASP cc_start: 0.8727 (m-30) cc_final: 0.8429 (m-30) REVERT: D 303 ASP cc_start: 0.8057 (p0) cc_final: 0.7759 (p0) REVERT: D 392 ASP cc_start: 0.7758 (t0) cc_final: 0.7390 (t0) REVERT: D 582 MET cc_start: 0.8959 (mmm) cc_final: 0.8602 (mmm) REVERT: D 617 LYS cc_start: 0.9406 (tptp) cc_final: 0.9198 (tppt) REVERT: D 656 ASP cc_start: 0.8977 (p0) cc_final: 0.8746 (p0) REVERT: E 215 ILE cc_start: 0.9169 (mp) cc_final: 0.8581 (tp) REVERT: E 342 PHE cc_start: 0.9100 (m-10) cc_final: 0.8757 (m-80) REVERT: E 582 MET cc_start: 0.9511 (mmp) cc_final: 0.9232 (mmm) REVERT: E 594 LEU cc_start: 0.8962 (tp) cc_final: 0.8608 (tt) REVERT: E 616 ARG cc_start: 0.9118 (ptm160) cc_final: 0.8357 (tmm-80) REVERT: E 623 LEU cc_start: 0.9727 (tt) cc_final: 0.9309 (tt) REVERT: E 656 ASP cc_start: 0.9483 (p0) cc_final: 0.9107 (p0) REVERT: E 709 PHE cc_start: 0.9018 (t80) cc_final: 0.8603 (t80) REVERT: E 747 MET cc_start: 0.8894 (mtt) cc_final: 0.8443 (mmm) REVERT: F 201 MET cc_start: 0.9017 (mpp) cc_final: 0.8568 (mpp) REVERT: F 284 LEU cc_start: 0.9278 (tp) cc_final: 0.9024 (tp) REVERT: F 331 TYR cc_start: 0.8389 (m-80) cc_final: 0.7384 (m-80) REVERT: F 510 MET cc_start: 0.9081 (tmm) cc_final: 0.8401 (tmm) REVERT: F 551 PHE cc_start: 0.9403 (m-80) cc_final: 0.9182 (m-10) REVERT: F 582 MET cc_start: 0.7405 (mpp) cc_final: 0.7045 (mpp) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.3863 time to fit residues: 184.2082 Evaluate side-chains 225 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 3.197 ------------------------------------------------------------------------------- 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: 6.9990 chunk 132 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053829 restraints weight = 161296.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055410 restraints weight = 100877.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056526 restraints weight = 70463.187| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27578 Z= 0.120 Angle : 0.597 9.249 37207 Z= 0.287 Chirality : 0.042 0.163 4245 Planarity : 0.004 0.055 4825 Dihedral : 8.271 174.210 3835 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.77 (0.15), residues: 3348 helix: 0.71 (0.12), residues: 1820 sheet: -0.08 (0.24), residues: 444 loop : 0.77 (0.22), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 491 HIS 0.003 0.001 HIS E 720 PHE 0.039 0.001 PHE C 791 TYR 0.026 0.001 TYR A 331 ARG 0.004 0.000 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1309) hydrogen bonds : angle 4.83998 ( 3840) covalent geometry : bond 0.00257 (27578) covalent geometry : angle 0.59656 (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 286 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.9187 (tmmt) cc_final: 0.8815 (tmmt) REVERT: A 331 TYR cc_start: 0.9064 (m-10) cc_final: 0.8793 (m-10) REVERT: A 354 HIS cc_start: 0.9292 (t-170) cc_final: 0.8962 (t-170) REVERT: A 379 MET cc_start: 0.9347 (mpp) cc_final: 0.8742 (mpp) REVERT: A 389 TYR cc_start: 0.8036 (m-10) cc_final: 0.7599 (m-10) REVERT: B 287 ASP cc_start: 0.9275 (m-30) cc_final: 0.8931 (m-30) REVERT: B 288 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 335 ASP cc_start: 0.9144 (t70) cc_final: 0.8671 (t0) REVERT: B 338 LEU cc_start: 0.9454 (mt) cc_final: 0.8891 (mt) REVERT: B 582 MET cc_start: 0.7964 (mmp) cc_final: 0.7644 (mmm) REVERT: B 623 LEU cc_start: 0.9106 (tp) cc_final: 0.8875 (tp) REVERT: C 227 GLU cc_start: 0.9180 (mp0) cc_final: 0.8876 (mp0) REVERT: C 379 MET cc_start: 0.9084 (pmm) cc_final: 0.8816 (pmm) REVERT: C 540 LYS cc_start: 0.9505 (pptt) cc_final: 0.9185 (pptt) REVERT: C 693 MET cc_start: 0.7902 (pmm) cc_final: 0.7641 (pmm) REVERT: C 730 MET cc_start: 0.9190 (mmp) cc_final: 0.8936 (mmp) REVERT: C 747 MET cc_start: 0.8356 (mtt) cc_final: 0.8100 (mtt) REVERT: D 201 MET cc_start: 0.8966 (mtp) cc_final: 0.8612 (mtm) REVERT: D 244 ASP cc_start: 0.8689 (m-30) cc_final: 0.8398 (m-30) REVERT: D 288 GLU cc_start: 0.8179 (pp20) cc_final: 0.7763 (pp20) REVERT: D 303 ASP cc_start: 0.8099 (p0) cc_final: 0.7757 (p0) REVERT: D 379 MET cc_start: 0.9240 (mpp) cc_final: 0.9001 (mpp) REVERT: D 392 ASP cc_start: 0.7888 (t0) cc_final: 0.7555 (t0) REVERT: D 582 MET cc_start: 0.9008 (mmm) cc_final: 0.8656 (mmm) REVERT: D 656 ASP cc_start: 0.8914 (p0) cc_final: 0.8695 (p0) REVERT: E 215 ILE cc_start: 0.9014 (mp) cc_final: 0.8353 (tp) REVERT: E 342 PHE cc_start: 0.9059 (m-10) cc_final: 0.8744 (m-80) REVERT: E 582 MET cc_start: 0.9551 (mmp) cc_final: 0.9259 (mmm) REVERT: E 594 LEU cc_start: 0.9011 (tp) cc_final: 0.8607 (tt) REVERT: E 616 ARG cc_start: 0.9122 (ptm160) cc_final: 0.8315 (tmm-80) REVERT: E 623 LEU cc_start: 0.9736 (tt) cc_final: 0.9275 (tt) REVERT: E 656 ASP cc_start: 0.9435 (p0) cc_final: 0.9061 (p0) REVERT: E 747 MET cc_start: 0.8880 (mtt) cc_final: 0.8448 (mmm) REVERT: F 201 MET cc_start: 0.8995 (mpp) cc_final: 0.8509 (mpp) REVERT: F 284 LEU cc_start: 0.9258 (tp) cc_final: 0.9033 (tp) REVERT: F 330 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8896 (ptmm) REVERT: F 331 TYR cc_start: 0.8368 (m-80) cc_final: 0.7316 (m-80) REVERT: F 410 MET cc_start: 0.9115 (mmp) cc_final: 0.8724 (mmt) REVERT: F 510 MET cc_start: 0.9081 (tmm) cc_final: 0.8400 (tmm) REVERT: F 551 PHE cc_start: 0.9388 (m-80) cc_final: 0.9058 (m-80) REVERT: F 582 MET cc_start: 0.7618 (mpp) cc_final: 0.7259 (mpp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3723 time to fit residues: 173.9088 Evaluate side-chains 222 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 4.196 ------------------------------------------------------------------------------- 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: 0.0000 chunk 297 optimal weight: 0.8980 chunk 193 optimal weight: 0.2980 chunk 81 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 E 720 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 = 0.3417 r_free = 0.3417 target = 0.066968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053619 restraints weight = 163897.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055201 restraints weight = 102158.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056346 restraints weight = 71741.557| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27578 Z= 0.130 Angle : 0.610 8.126 37207 Z= 0.294 Chirality : 0.042 0.181 4245 Planarity : 0.004 0.054 4825 Dihedral : 8.061 164.831 3835 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.15), residues: 3348 helix: 0.77 (0.12), residues: 1812 sheet: -0.16 (0.24), residues: 455 loop : 0.80 (0.22), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 491 HIS 0.005 0.001 HIS C 290 PHE 0.034 0.001 PHE C 791 TYR 0.022 0.001 TYR D 331 ARG 0.006 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 1309) hydrogen bonds : angle 4.83168 ( 3840) covalent geometry : bond 0.00278 (27578) covalent geometry : angle 0.60968 (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 284 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 TYR cc_start: 0.9281 (t80) cc_final: 0.9074 (t80) REVERT: A 354 HIS cc_start: 0.9231 (t-170) cc_final: 0.8950 (t-170) REVERT: A 379 MET cc_start: 0.9365 (mpp) cc_final: 0.8741 (mpp) REVERT: A 389 TYR cc_start: 0.8061 (m-10) cc_final: 0.7600 (m-10) REVERT: A 625 ASP cc_start: 0.8241 (t70) cc_final: 0.7987 (t70) REVERT: B 287 ASP cc_start: 0.9272 (m-30) cc_final: 0.8939 (m-30) REVERT: B 288 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 338 LEU cc_start: 0.9500 (mt) cc_final: 0.9271 (mt) REVERT: B 379 MET cc_start: 0.9036 (pmm) cc_final: 0.8779 (pmm) REVERT: B 582 MET cc_start: 0.7965 (mmp) cc_final: 0.7689 (mmm) REVERT: B 623 LEU cc_start: 0.9095 (tp) cc_final: 0.8868 (tp) REVERT: C 227 GLU cc_start: 0.9464 (mp0) cc_final: 0.9032 (mp0) REVERT: C 271 LYS cc_start: 0.9578 (tptp) cc_final: 0.9303 (tptp) REVERT: C 287 ASP cc_start: 0.8455 (t0) cc_final: 0.8225 (p0) REVERT: C 379 MET cc_start: 0.9101 (pmm) cc_final: 0.8805 (pmm) REVERT: C 510 MET cc_start: 0.9319 (ppp) cc_final: 0.9051 (ppp) REVERT: C 540 LYS cc_start: 0.9439 (pptt) cc_final: 0.9102 (pptt) REVERT: C 635 TYR cc_start: 0.8473 (m-80) cc_final: 0.8069 (m-80) REVERT: C 730 MET cc_start: 0.9187 (mmp) cc_final: 0.8938 (mmp) REVERT: C 747 MET cc_start: 0.8263 (mtt) cc_final: 0.7974 (mtt) REVERT: D 201 MET cc_start: 0.8970 (mtp) cc_final: 0.8632 (mtm) REVERT: D 244 ASP cc_start: 0.8724 (m-30) cc_final: 0.8417 (m-30) REVERT: D 290 HIS cc_start: 0.8928 (p-80) cc_final: 0.8582 (p-80) REVERT: D 303 ASP cc_start: 0.8152 (p0) cc_final: 0.7866 (p0) REVERT: D 379 MET cc_start: 0.9366 (mpp) cc_final: 0.9030 (mpp) REVERT: D 392 ASP cc_start: 0.7897 (t0) cc_final: 0.7563 (t0) REVERT: D 582 MET cc_start: 0.8971 (mmm) cc_final: 0.8630 (mmm) REVERT: D 656 ASP cc_start: 0.8969 (p0) cc_final: 0.8728 (p0) REVERT: E 215 ILE cc_start: 0.8759 (mp) cc_final: 0.8124 (tp) REVERT: E 329 ARG cc_start: 0.9157 (mtm110) cc_final: 0.8769 (mmm160) REVERT: E 342 PHE cc_start: 0.9058 (m-10) cc_final: 0.8531 (m-80) REVERT: E 582 MET cc_start: 0.9528 (mmp) cc_final: 0.9325 (mmm) REVERT: E 594 LEU cc_start: 0.9120 (tp) cc_final: 0.8736 (tp) REVERT: E 616 ARG cc_start: 0.9165 (ptm160) cc_final: 0.8336 (tmm-80) REVERT: E 623 LEU cc_start: 0.9730 (tt) cc_final: 0.9381 (tt) REVERT: E 747 MET cc_start: 0.8921 (mtt) cc_final: 0.8467 (mmm) REVERT: F 201 MET cc_start: 0.8969 (mpp) cc_final: 0.8484 (mpp) REVERT: F 284 LEU cc_start: 0.9275 (tp) cc_final: 0.9073 (tp) REVERT: F 330 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8798 (ptmm) REVERT: F 331 TYR cc_start: 0.8446 (m-80) cc_final: 0.7728 (m-80) REVERT: F 410 MET cc_start: 0.9136 (mmp) cc_final: 0.8777 (mmt) REVERT: F 510 MET cc_start: 0.9109 (tmm) cc_final: 0.8572 (tmm) REVERT: F 551 PHE cc_start: 0.9412 (m-80) cc_final: 0.9095 (m-80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.4060 time to fit residues: 185.0304 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 : 3.723 ------------------------------------------------------------------------------- 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: 0.0270 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 0.0040 chunk 333 optimal weight: 0.3980 chunk 5 optimal weight: 10.0000 chunk 281 optimal weight: 0.0980 chunk 186 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 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 = 0.3438 r_free = 0.3438 target = 0.067744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054372 restraints weight = 158315.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055988 restraints weight = 97980.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.057119 restraints weight = 68350.022| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27578 Z= 0.100 Angle : 0.601 7.891 37207 Z= 0.286 Chirality : 0.042 0.301 4245 Planarity : 0.004 0.055 4825 Dihedral : 7.643 159.152 3835 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.89 (0.15), residues: 3348 helix: 0.81 (0.12), residues: 1817 sheet: 0.07 (0.25), residues: 417 loop : 0.73 (0.22), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 491 HIS 0.005 0.001 HIS C 290 PHE 0.032 0.001 PHE C 791 TYR 0.018 0.001 TYR D 331 ARG 0.006 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 1309) hydrogen bonds : angle 4.72411 ( 3840) covalent geometry : bond 0.00216 (27578) covalent geometry : angle 0.60106 (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 297 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 3.109 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: 0.9695 (mp) cc_final: 0.9479 (mp) REVERT: A 250 LEU cc_start: 0.9296 (tt) cc_final: 0.8545 (mm) REVERT: A 354 HIS cc_start: 0.9220 (t-170) cc_final: 0.8966 (t-170) REVERT: A 379 MET cc_start: 0.9366 (mpp) cc_final: 0.8742 (mpp) REVERT: A 389 TYR cc_start: 0.8049 (m-10) cc_final: 0.7575 (m-10) REVERT: B 198 GLU cc_start: 0.9144 (pt0) cc_final: 0.8835 (tp30) REVERT: B 287 ASP cc_start: 0.9253 (m-30) cc_final: 0.8872 (m-30) REVERT: B 288 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 338 LEU cc_start: 0.9430 (mt) cc_final: 0.9189 (mt) REVERT: B 582 MET cc_start: 0.8032 (mmp) cc_final: 0.7782 (mmm) REVERT: B 623 LEU cc_start: 0.9098 (tp) cc_final: 0.8886 (tp) REVERT: C 227 GLU cc_start: 0.9252 (mp0) cc_final: 0.9047 (mp0) REVERT: C 379 MET cc_start: 0.9144 (pmm) cc_final: 0.8806 (pmm) REVERT: C 410 MET cc_start: 0.9260 (mmp) cc_final: 0.8928 (mmt) REVERT: C 540 LYS cc_start: 0.9438 (pptt) cc_final: 0.9097 (pptt) REVERT: C 635 TYR cc_start: 0.8438 (m-80) cc_final: 0.8083 (m-80) REVERT: C 730 MET cc_start: 0.9143 (mmp) cc_final: 0.8928 (mmp) REVERT: C 747 MET cc_start: 0.8254 (mtt) cc_final: 0.7943 (mtt) REVERT: D 201 MET cc_start: 0.8929 (mtp) cc_final: 0.8618 (mtp) REVERT: D 244 ASP cc_start: 0.8765 (m-30) cc_final: 0.8464 (m-30) REVERT: D 288 GLU cc_start: 0.7942 (pp20) cc_final: 0.7550 (pp20) REVERT: D 303 ASP cc_start: 0.7753 (p0) cc_final: 0.7486 (p0) REVERT: D 379 MET cc_start: 0.9270 (mpp) cc_final: 0.8967 (mpp) REVERT: D 578 ILE cc_start: 0.9291 (mm) cc_final: 0.9019 (mm) REVERT: D 582 MET cc_start: 0.8915 (mmm) cc_final: 0.8610 (mmm) REVERT: D 627 ILE cc_start: 0.9410 (tp) cc_final: 0.9207 (tp) REVERT: D 656 ASP cc_start: 0.8921 (p0) cc_final: 0.8696 (p0) REVERT: E 215 ILE cc_start: 0.8662 (mp) cc_final: 0.8079 (tp) REVERT: E 328 TYR cc_start: 0.9379 (t80) cc_final: 0.8627 (t80) REVERT: E 329 ARG cc_start: 0.9162 (mtm110) cc_final: 0.8764 (mmm160) REVERT: E 342 PHE cc_start: 0.9048 (m-10) cc_final: 0.8638 (m-80) REVERT: E 582 MET cc_start: 0.9514 (mmp) cc_final: 0.9296 (mmm) REVERT: E 594 LEU cc_start: 0.9112 (tp) cc_final: 0.8732 (tp) REVERT: E 616 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8318 (tmm-80) REVERT: E 623 LEU cc_start: 0.9730 (tt) cc_final: 0.9375 (tt) REVERT: E 747 MET cc_start: 0.8940 (mtt) cc_final: 0.8502 (mmm) REVERT: F 201 MET cc_start: 0.8937 (mpp) cc_final: 0.8511 (mpp) REVERT: F 284 LEU cc_start: 0.9259 (tp) cc_final: 0.9011 (tp) REVERT: F 330 LYS cc_start: 0.9165 (ptmm) cc_final: 0.8878 (ptmm) REVERT: F 331 TYR cc_start: 0.8362 (m-80) cc_final: 0.7562 (m-80) REVERT: F 510 MET cc_start: 0.9115 (tmm) cc_final: 0.8640 (tmm) REVERT: F 551 PHE cc_start: 0.9387 (m-80) cc_final: 0.9052 (m-80) REVERT: F 730 MET cc_start: 0.8199 (mmt) cc_final: 0.7624 (mmt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3715 time to fit residues: 176.4078 Evaluate side-chains 228 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 3.084 ------------------------------------------------------------------------------- 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: 7.9990 chunk 262 optimal weight: 0.1980 chunk 285 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 260 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 HIS ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 290 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053843 restraints weight = 160437.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055425 restraints weight = 99396.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056546 restraints weight = 69405.445| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27578 Z= 0.117 Angle : 0.611 7.124 37207 Z= 0.295 Chirality : 0.042 0.246 4245 Planarity : 0.004 0.094 4825 Dihedral : 7.470 149.147 3835 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 0.93 (0.15), residues: 3348 helix: 0.85 (0.12), residues: 1817 sheet: -0.07 (0.24), residues: 435 loop : 0.84 (0.22), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 491 HIS 0.005 0.001 HIS C 290 PHE 0.033 0.001 PHE C 791 TYR 0.020 0.001 TYR D 331 ARG 0.010 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.02891 ( 1309) hydrogen bonds : angle 4.72660 ( 3840) covalent geometry : bond 0.00256 (27578) covalent geometry : angle 0.61120 (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 282 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.9321 (t-170) cc_final: 0.8969 (t-170) REVERT: A 379 MET cc_start: 0.9383 (mpp) cc_final: 0.8730 (mpp) REVERT: A 389 TYR cc_start: 0.8075 (m-10) cc_final: 0.7593 (m-10) REVERT: A 625 ASP cc_start: 0.8232 (t70) cc_final: 0.7960 (t70) REVERT: A 662 LEU cc_start: 0.9407 (mt) cc_final: 0.9188 (mm) REVERT: B 287 ASP cc_start: 0.9254 (m-30) cc_final: 0.8901 (m-30) REVERT: B 288 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 338 LEU cc_start: 0.9478 (mt) cc_final: 0.9254 (mt) REVERT: B 379 MET cc_start: 0.8968 (pmm) cc_final: 0.8719 (pmm) REVERT: B 582 MET cc_start: 0.8096 (mmp) cc_final: 0.7826 (mmm) REVERT: B 623 LEU cc_start: 0.9105 (tp) cc_final: 0.8885 (tp) REVERT: C 227 GLU cc_start: 0.9190 (mp0) cc_final: 0.8948 (mp0) REVERT: C 379 MET cc_start: 0.9051 (pmm) cc_final: 0.8718 (pmm) REVERT: C 410 MET cc_start: 0.9292 (mmp) cc_final: 0.8972 (mmt) REVERT: C 540 LYS cc_start: 0.9456 (pptt) cc_final: 0.9124 (pptt) REVERT: C 616 ARG cc_start: 0.8928 (mpt180) cc_final: 0.8150 (mmt-90) REVERT: C 635 TYR cc_start: 0.8200 (m-80) cc_final: 0.7783 (m-80) REVERT: C 730 MET cc_start: 0.9145 (mmp) cc_final: 0.8912 (mmp) REVERT: C 747 MET cc_start: 0.8325 (mtt) cc_final: 0.7982 (mtt) REVERT: D 201 MET cc_start: 0.8999 (mtp) cc_final: 0.8663 (mtp) REVERT: D 244 ASP cc_start: 0.8750 (m-30) cc_final: 0.8451 (m-30) REVERT: D 303 ASP cc_start: 0.7830 (p0) cc_final: 0.7577 (p0) REVERT: D 582 MET cc_start: 0.8934 (mmm) cc_final: 0.8662 (mmm) REVERT: D 656 ASP cc_start: 0.8957 (p0) cc_final: 0.8725 (p0) REVERT: E 215 ILE cc_start: 0.8692 (mp) cc_final: 0.7973 (tp) REVERT: E 342 PHE cc_start: 0.9036 (m-10) cc_final: 0.8625 (m-80) REVERT: E 582 MET cc_start: 0.9493 (mmp) cc_final: 0.9055 (mmp) REVERT: E 594 LEU cc_start: 0.9153 (tp) cc_final: 0.8749 (tp) REVERT: E 616 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8380 (tmm-80) REVERT: E 623 LEU cc_start: 0.9737 (tt) cc_final: 0.9371 (tt) REVERT: E 747 MET cc_start: 0.9005 (mtt) cc_final: 0.8532 (mmm) REVERT: F 183 MET cc_start: 0.8522 (mmp) cc_final: 0.8317 (mmp) REVERT: F 201 MET cc_start: 0.8962 (mpp) cc_final: 0.8510 (mpp) REVERT: F 284 LEU cc_start: 0.9265 (tp) cc_final: 0.9061 (tp) REVERT: F 330 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8899 (ptmm) REVERT: F 331 TYR cc_start: 0.8390 (m-80) cc_final: 0.7701 (m-80) REVERT: F 510 MET cc_start: 0.9133 (tmm) cc_final: 0.8661 (tmm) REVERT: F 551 PHE cc_start: 0.9319 (m-80) cc_final: 0.8978 (m-80) REVERT: F 582 MET cc_start: 0.7439 (mpp) cc_final: 0.7104 (mpp) REVERT: F 730 MET cc_start: 0.8239 (mmt) cc_final: 0.7658 (mmt) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3746 time to fit residues: 170.5174 Evaluate side-chains 225 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 3.557 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 310 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 195 optimal weight: 0.4980 chunk 264 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** 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 = 0.3427 r_free = 0.3427 target = 0.067244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053905 restraints weight = 161542.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055508 restraints weight = 100723.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056654 restraints weight = 70462.444| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27578 Z= 0.115 Angle : 0.618 9.992 37207 Z= 0.297 Chirality : 0.043 0.229 4245 Planarity : 0.004 0.059 4825 Dihedral : 7.396 146.935 3835 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.89 (0.15), residues: 3348 helix: 0.81 (0.12), residues: 1828 sheet: -0.03 (0.24), residues: 455 loop : 0.84 (0.22), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 491 HIS 0.013 0.001 HIS C 290 PHE 0.034 0.001 PHE F 497 TYR 0.022 0.001 TYR A 328 ARG 0.008 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 1309) hydrogen bonds : angle 4.76968 ( 3840) covalent geometry : bond 0.00249 (27578) covalent geometry : angle 0.61810 (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 286 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8018 (ttp80) REVERT: A 178 LEU cc_start: 0.9698 (mp) cc_final: 0.9475 (mp) REVERT: A 290 HIS cc_start: 0.7913 (p90) cc_final: 0.7490 (p-80) REVERT: A 354 HIS cc_start: 0.9306 (t-170) cc_final: 0.8954 (t-170) REVERT: A 379 MET cc_start: 0.9380 (mpp) cc_final: 0.8757 (mpp) REVERT: A 389 TYR cc_start: 0.8100 (m-10) cc_final: 0.7602 (m-10) REVERT: B 198 GLU cc_start: 0.9131 (pt0) cc_final: 0.8843 (tp30) REVERT: B 287 ASP cc_start: 0.9401 (m-30) cc_final: 0.9002 (m-30) REVERT: B 288 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 338 LEU cc_start: 0.9482 (mt) cc_final: 0.9266 (mt) REVERT: B 582 MET cc_start: 0.8086 (mmp) cc_final: 0.7830 (mmm) REVERT: B 623 LEU cc_start: 0.9084 (tp) cc_final: 0.8855 (tp) REVERT: C 201 MET cc_start: 0.8921 (mtm) cc_final: 0.8690 (mtp) REVERT: C 227 GLU cc_start: 0.9338 (mp0) cc_final: 0.9011 (pm20) REVERT: C 290 HIS cc_start: 0.7879 (p-80) cc_final: 0.7416 (p-80) REVERT: C 379 MET cc_start: 0.9090 (pmm) cc_final: 0.8693 (pmm) REVERT: C 540 LYS cc_start: 0.9465 (pptt) cc_final: 0.9136 (pptt) REVERT: C 635 TYR cc_start: 0.8366 (m-80) cc_final: 0.7993 (m-80) REVERT: C 693 MET cc_start: 0.7955 (pmm) cc_final: 0.7713 (pmm) REVERT: C 730 MET cc_start: 0.9135 (mmp) cc_final: 0.8926 (mmp) REVERT: C 747 MET cc_start: 0.8314 (mtt) cc_final: 0.7968 (mtt) REVERT: D 201 MET cc_start: 0.9005 (mtp) cc_final: 0.8469 (ptm) REVERT: D 244 ASP cc_start: 0.8756 (m-30) cc_final: 0.8446 (m-30) REVERT: D 288 GLU cc_start: 0.7662 (pp20) cc_final: 0.7307 (pp20) REVERT: D 303 ASP cc_start: 0.7876 (p0) cc_final: 0.7633 (p0) REVERT: D 582 MET cc_start: 0.8951 (mmm) cc_final: 0.8679 (mmm) REVERT: D 656 ASP cc_start: 0.8932 (p0) cc_final: 0.8731 (p0) REVERT: E 215 ILE cc_start: 0.8686 (mp) cc_final: 0.8015 (tp) REVERT: E 342 PHE cc_start: 0.9040 (m-10) cc_final: 0.8614 (m-80) REVERT: E 582 MET cc_start: 0.9473 (mmp) cc_final: 0.9261 (mmm) REVERT: E 594 LEU cc_start: 0.9174 (tp) cc_final: 0.8763 (tp) REVERT: E 616 ARG cc_start: 0.9143 (ptm160) cc_final: 0.8377 (tmm-80) REVERT: E 623 LEU cc_start: 0.9725 (tt) cc_final: 0.9340 (tt) REVERT: E 747 MET cc_start: 0.8990 (mtt) cc_final: 0.8536 (mmm) REVERT: F 183 MET cc_start: 0.8534 (mmp) cc_final: 0.8328 (mmp) REVERT: F 201 MET cc_start: 0.8975 (mpp) cc_final: 0.8521 (mpp) REVERT: F 284 LEU cc_start: 0.9253 (tp) cc_final: 0.9048 (tp) REVERT: F 330 LYS cc_start: 0.9168 (ptmm) cc_final: 0.8891 (ptmm) REVERT: F 331 TYR cc_start: 0.8382 (m-80) cc_final: 0.7685 (m-80) REVERT: F 410 MET cc_start: 0.9479 (mmm) cc_final: 0.9213 (mmt) REVERT: F 510 MET cc_start: 0.9163 (tmm) cc_final: 0.8780 (tmm) REVERT: F 551 PHE cc_start: 0.9328 (m-80) cc_final: 0.9040 (m-80) REVERT: F 582 MET cc_start: 0.7457 (mpp) cc_final: 0.7117 (mpp) REVERT: F 730 MET cc_start: 0.8339 (mmt) cc_final: 0.7683 (mmt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3931 time to fit residues: 181.4917 Evaluate side-chains 225 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 3.346 ------------------------------------------------------------------------------- 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: 0.9980 chunk 226 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 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 = 0.3426 r_free = 0.3426 target = 0.067124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053803 restraints weight = 159857.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055420 restraints weight = 98985.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056578 restraints weight = 68997.211| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27578 Z= 0.117 Angle : 0.630 9.501 37207 Z= 0.304 Chirality : 0.043 0.222 4245 Planarity : 0.004 0.053 4825 Dihedral : 7.334 145.853 3835 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.91 (0.15), residues: 3348 helix: 0.82 (0.12), residues: 1827 sheet: -0.05 (0.24), residues: 447 loop : 0.85 (0.22), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 491 HIS 0.009 0.001 HIS C 290 PHE 0.032 0.001 PHE C 791 TYR 0.022 0.002 TYR D 331 ARG 0.007 0.000 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 1309) hydrogen bonds : angle 4.78033 ( 3840) covalent geometry : bond 0.00255 (27578) covalent geometry : angle 0.62974 (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 283 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8164 (ttp80) REVERT: A 178 LEU cc_start: 0.9699 (mp) cc_final: 0.9488 (mp) REVERT: A 331 TYR cc_start: 0.8902 (m-10) cc_final: 0.8331 (m-10) REVERT: A 354 HIS cc_start: 0.9343 (t-170) cc_final: 0.8973 (t-170) REVERT: A 379 MET cc_start: 0.9397 (mpp) cc_final: 0.8709 (mpp) REVERT: A 389 TYR cc_start: 0.8119 (m-10) cc_final: 0.7605 (m-10) REVERT: A 622 VAL cc_start: 0.8786 (t) cc_final: 0.8436 (p) REVERT: B 198 GLU cc_start: 0.9151 (pt0) cc_final: 0.8849 (tp30) REVERT: B 287 ASP cc_start: 0.9410 (m-30) cc_final: 0.9035 (m-30) REVERT: B 288 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7897 (mm-30) REVERT: B 338 LEU cc_start: 0.9488 (mt) cc_final: 0.9269 (mt) REVERT: B 582 MET cc_start: 0.8079 (mmp) cc_final: 0.7827 (mmm) REVERT: B 623 LEU cc_start: 0.9086 (tp) cc_final: 0.8861 (tp) REVERT: C 201 MET cc_start: 0.8939 (mtm) cc_final: 0.8670 (mtp) REVERT: C 227 GLU cc_start: 0.9507 (mp0) cc_final: 0.9138 (pm20) REVERT: C 271 LYS cc_start: 0.9644 (tptt) cc_final: 0.9433 (tppt) REVERT: C 379 MET cc_start: 0.9118 (pmm) cc_final: 0.8716 (pmm) REVERT: C 410 MET cc_start: 0.9209 (mmp) cc_final: 0.8964 (mmt) REVERT: C 510 MET cc_start: 0.9310 (ppp) cc_final: 0.9090 (ppp) REVERT: C 540 LYS cc_start: 0.9442 (pptt) cc_final: 0.9095 (pptt) REVERT: C 635 TYR cc_start: 0.8396 (m-80) cc_final: 0.8041 (m-80) REVERT: C 693 MET cc_start: 0.7977 (pmm) cc_final: 0.7730 (pmm) REVERT: C 730 MET cc_start: 0.9139 (mmp) cc_final: 0.8932 (mmp) REVERT: C 747 MET cc_start: 0.8320 (mtt) cc_final: 0.7965 (mtt) REVERT: D 201 MET cc_start: 0.9043 (mtp) cc_final: 0.8512 (ptm) REVERT: D 244 ASP cc_start: 0.8799 (m-30) cc_final: 0.8477 (m-30) REVERT: D 288 GLU cc_start: 0.7863 (pp20) cc_final: 0.7377 (pp20) REVERT: D 290 HIS cc_start: 0.9014 (p-80) cc_final: 0.8744 (p-80) REVERT: D 303 ASP cc_start: 0.7866 (p0) cc_final: 0.7651 (p0) REVERT: D 582 MET cc_start: 0.9003 (mmm) cc_final: 0.8696 (mmm) REVERT: D 656 ASP cc_start: 0.8966 (p0) cc_final: 0.8726 (p0) REVERT: E 215 ILE cc_start: 0.8716 (mp) cc_final: 0.7943 (tp) REVERT: E 227 GLU cc_start: 0.9218 (mp0) cc_final: 0.8923 (pm20) REVERT: E 291 THR cc_start: 0.9672 (p) cc_final: 0.8883 (p) REVERT: E 342 PHE cc_start: 0.9004 (m-10) cc_final: 0.8562 (m-80) REVERT: E 510 MET cc_start: 0.9194 (ppp) cc_final: 0.8990 (ppp) REVERT: E 582 MET cc_start: 0.9499 (mmp) cc_final: 0.9263 (mmm) REVERT: E 594 LEU cc_start: 0.9176 (tp) cc_final: 0.8769 (tp) REVERT: E 616 ARG cc_start: 0.9167 (ptm160) cc_final: 0.8442 (tmm-80) REVERT: E 623 LEU cc_start: 0.9739 (tt) cc_final: 0.9348 (tt) REVERT: E 747 MET cc_start: 0.9003 (mtt) cc_final: 0.8546 (mmm) REVERT: F 201 MET cc_start: 0.8986 (mpp) cc_final: 0.8398 (mpp) REVERT: F 284 LEU cc_start: 0.9251 (tp) cc_final: 0.9043 (tp) REVERT: F 330 LYS cc_start: 0.9159 (ptmm) cc_final: 0.8878 (ptmm) REVERT: F 331 TYR cc_start: 0.8389 (m-80) cc_final: 0.7714 (m-80) REVERT: F 379 MET cc_start: 0.8639 (ppp) cc_final: 0.8344 (ppp) REVERT: F 510 MET cc_start: 0.9157 (tmm) cc_final: 0.8786 (tmm) REVERT: F 551 PHE cc_start: 0.9334 (m-80) cc_final: 0.9057 (m-80) REVERT: F 582 MET cc_start: 0.7321 (mpp) cc_final: 0.6953 (mpp) REVERT: F 734 MET cc_start: 0.9107 (mpp) cc_final: 0.8551 (mpp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.4033 time to fit residues: 183.3978 Evaluate side-chains 222 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 3.042 ------------------------------------------------------------------------------- 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: 0.3980 chunk 294 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** C 290 HIS ** 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** C 651 GLN E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053431 restraints weight = 161621.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055041 restraints weight = 101500.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056149 restraints weight = 70789.876| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27578 Z= 0.126 Angle : 0.640 9.159 37207 Z= 0.310 Chirality : 0.043 0.229 4245 Planarity : 0.004 0.053 4825 Dihedral : 7.300 144.551 3835 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.91 (0.15), residues: 3348 helix: 0.82 (0.12), residues: 1828 sheet: -0.04 (0.24), residues: 455 loop : 0.87 (0.22), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 491 HIS 0.016 0.001 HIS C 290 PHE 0.032 0.001 PHE C 791 TYR 0.024 0.002 TYR C 331 ARG 0.007 0.000 ARG F 712 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 1309) hydrogen bonds : angle 4.81156 ( 3840) covalent geometry : bond 0.00272 (27578) covalent geometry : angle 0.63989 (37207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7976.92 seconds wall clock time: 140 minutes 27.68 seconds (8427.68 seconds total)