Starting phenix.real_space_refine on Fri Mar 6 02:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8u_15240/03_2026/8a8u_15240.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.058 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 17023 2.51 5 N 4833 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27129 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: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} 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: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4329 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 527} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.23, per 1000 atoms: 0.23 Number of scatterers: 27129 At special positions: 0 Unit cell: (119.7, 135.09, 150.48, 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 5187 8.00 N 4833 7.00 C 17023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 28 sheets defined 59.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 170 through 174 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 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.860A pdb=" N VAL A 293 " --> 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 340 Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.608A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 4.053A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 415 removed outlier: 4.150A pdb=" N MET A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.676A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.796A pdb=" N LEU A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.750A 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 Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.512A 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 removed outlier: 3.725A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) 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 781 removed outlier: 3.800A pdb=" N GLN A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.631A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.769A 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: 3.672A 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 256 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.575A pdb=" N VAL B 293 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.598A 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 removed outlier: 3.958A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 removed outlier: 4.890A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 5.069A 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 509 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 521 through 537 Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.730A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 589 through 596 removed outlier: 4.287A pdb=" N ARG B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.528A pdb=" N GLU B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.591A pdb=" N ALA B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 4.096A pdb=" N TYR B 635 " --> pdb=" O HIS B 631 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.628A pdb=" N LEU B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.993A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.696A 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 169 through 174 removed outlier: 4.022A pdb=" N GLN C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 174' Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.549A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.725A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 280 removed outlier: 3.757A pdb=" N PHE C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 removed outlier: 3.757A pdb=" N VAL C 293 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix removed outlier: 3.772A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.514A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.674A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 396 through 415 Processing helix chain 'C' and resid 480 through 493 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.503A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.533A pdb=" N VAL C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.879A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.219A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.684A pdb=" N GLU C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 644 removed outlier: 4.344A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.620A pdb=" N LEU C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 713 " --> pdb=" O PHE C 709 " (cutoff:3.500A) 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 774 through 781 Processing helix chain 'C' and resid 781 through 791 removed outlier: 3.743A pdb=" N PHE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.862A pdb=" N GLU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.957A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.797A pdb=" N LYS D 243 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.703A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Proline residue: D 310 - end of helix removed outlier: 3.878A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 removed outlier: 4.016A pdb=" N ILE D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 371 removed outlier: 4.774A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.638A pdb=" N MET D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 415 removed outlier: 4.020A pdb=" N MET D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) 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 515 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 558 through 571 removed outlier: 3.539A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.719A pdb=" N ALA D 576 " --> pdb=" O ASP D 573 " (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 Processing helix chain 'D' and resid 591 through 596 removed outlier: 4.222A 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 627 through 630 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 634 through 642 removed outlier: 3.937A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.361A 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 removed outlier: 3.567A pdb=" N LEU D 710 " --> pdb=" O ARG D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 744 removed outlier: 4.004A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.630A 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 removed outlier: 3.946A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 221 through 236 removed outlier: 4.213A 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 289 through 293 removed outlier: 3.592A pdb=" N VAL E 293 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.639A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 361 Processing helix chain 'E' and resid 362 through 371 removed outlier: 4.081A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.963A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 415 removed outlier: 3.874A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 493 removed outlier: 3.682A pdb=" N ILE E 484 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 removed outlier: 3.852A pdb=" N ARG E 509 " --> pdb=" O THR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 558 through 572 removed outlier: 3.651A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.576A pdb=" N ALA E 576 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.904A 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 627 through 630 Processing helix chain 'E' and resid 631 through 644 removed outlier: 3.995A pdb=" N TYR E 635 " --> pdb=" O HIS E 631 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.548A 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 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 removed outlier: 3.687A pdb=" N ILE E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 791 removed outlier: 3.764A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.532A pdb=" N GLU F 184 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 223 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 288 through 293 removed outlier: 4.009A pdb=" N LEU F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 314 removed outlier: 3.722A 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 332 Processing helix chain 'F' and resid 351 through 371 removed outlier: 4.580A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 4.837A 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 415 removed outlier: 3.998A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 493 Processing helix chain 'F' and resid 502 through 508 removed outlier: 3.839A pdb=" N ARG F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 518 removed outlier: 3.926A pdb=" N GLU F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG F 517 " --> pdb=" O GLU F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.729A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 removed outlier: 3.534A pdb=" N PHE F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 617 removed outlier: 3.615A pdb=" N LYS F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 630 removed outlier: 3.612A pdb=" N ALA F 630 " --> pdb=" O ILE F 627 " (cutoff:3.500A) No H-bonds generated for '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: 3.790A pdb=" N LEU F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 745 removed outlier: 4.174A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.471A 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 781 removed outlier: 3.629A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 792 removed outlier: 3.624A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 251 removed outlier: 8.607A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 323 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 214 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 213 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 7.115A 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: 3.701A pdb=" N ILE A 580 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 625 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 665 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.087A 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 removed outlier: 3.852A pdb=" N LEU A 647 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 655 " --> pdb=" O LEU A 647 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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: 4.610A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 322 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.871A 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: 6.074A pdb=" N VAL B 622 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 665 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 624 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 5.759A 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: 3.785A pdb=" N ASP B 805 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 3.674A 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: 5.043A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 322 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 213 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 347 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.876A 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: 6.859A 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: 5.950A pdb=" N GLY C 547 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 664 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 549 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER C 666 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE C 551 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER C 548 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE C 717 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 550 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.718A pdb=" N LEU C 647 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.353A pdb=" N ALA C 748 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL C 802 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 750 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N VAL C 804 " --> pdb=" O VAL C 750 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 805 " --> pdb=" O VAL C 817 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 817 " --> pdb=" O ASP C 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.627A pdb=" N GLY D 216 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 373 through 374 removed outlier: 6.689A pdb=" N SER D 373 " --> pdb=" O VAL D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 578 through 581 Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.575A pdb=" N LEU D 647 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 748 through 751 removed outlier: 3.759A pdb=" N VAL D 817 " --> pdb=" O ASP D 805 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.553A pdb=" N GLN E 246 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE E 285 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR E 248 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP E 287 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU E 250 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 373 through 374 removed outlier: 7.064A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.814A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 547 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER E 548 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 717 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE E 550 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 749 through 751 removed outlier: 3.555A pdb=" N ASP E 805 " --> pdb=" O VAL E 817 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 817 " --> pdb=" O ASP E 805 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 175 through 177 removed outlier: 5.833A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP F 287 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LEU F 250 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE F 282 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE F 286 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 216 " --> pdb=" O THR F 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 345 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL F 213 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 347 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 215 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 373 through 374 removed outlier: 7.264A 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 578 through 581 removed outlier: 6.578A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 622 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 663 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY F 547 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE F 664 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE F 549 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER F 666 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE F 551 " --> pdb=" O SER F 666 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER F 548 " --> pdb=" O ASP F 715 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 717 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE F 550 " --> pdb=" O ILE F 717 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 749 through 750 removed outlier: 3.778A pdb=" N ASP F 805 " --> pdb=" O VAL F 817 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 817 " --> pdb=" O ASP F 805 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3861 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: 4.94 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7740 1.33 - 1.46: 4469 1.46 - 1.58: 15146 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27518 Sorted by residual: bond pdb=" C GLY A 553 " pdb=" N PRO A 554 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.42e+00 bond pdb=" CB PRO F 218 " pdb=" CG PRO F 218 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C PRO A 554 " pdb=" O PRO A 554 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.18e-02 7.18e+03 3.18e+00 bond pdb=" CA ASP B 815 " pdb=" C ASP B 815 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.66e-02 3.63e+03 2.18e+00 bond pdb=" C ARG B 544 " pdb=" N PRO B 545 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.21e-02 6.83e+03 2.17e+00 ... (remaining 27513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 36507 2.79 - 5.57: 533 5.57 - 8.36: 68 8.36 - 11.14: 11 11.14 - 13.93: 2 Bond angle restraints: 37121 Sorted by residual: angle pdb=" N VAL D 557 " pdb=" CA VAL D 557 " pdb=" C VAL D 557 " ideal model delta sigma weight residual 112.17 105.11 7.06 9.50e-01 1.11e+00 5.53e+01 angle pdb=" CA PRO F 218 " pdb=" N PRO F 218 " pdb=" CD PRO F 218 " ideal model delta sigma weight residual 112.00 104.10 7.90 1.40e+00 5.10e-01 3.18e+01 angle pdb=" CB MET B 415 " pdb=" CG MET B 415 " pdb=" SD MET B 415 " ideal model delta sigma weight residual 112.70 126.63 -13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N GLY C 769 " pdb=" CA GLY C 769 " pdb=" C GLY C 769 " ideal model delta sigma weight residual 110.29 104.48 5.81 1.28e+00 6.10e-01 2.06e+01 angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 113.53 109.09 4.44 9.80e-01 1.04e+00 2.05e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 16209 30.75 - 61.51: 573 61.51 - 92.26: 43 92.26 - 123.01: 9 123.01 - 153.76: 6 Dihedral angle restraints: 16840 sinusoidal: 7096 harmonic: 9744 Sorted by residual: 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 93.77 -153.76 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 80.48 -140.48 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 79.49 -139.48 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3624 0.068 - 0.136: 580 0.136 - 0.205: 24 0.205 - 0.273: 3 0.273 - 0.341: 2 Chirality restraints: 4233 Sorted by residual: chirality pdb=" CB VAL B 256 " pdb=" CA VAL B 256 " pdb=" CG1 VAL B 256 " pdb=" CG2 VAL B 256 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE C 716 " pdb=" CA ILE C 716 " pdb=" CG1 ILE C 716 " pdb=" CG2 ILE C 716 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4230 not shown) Planarity restraints: 4813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 217 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO F 218 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO F 218 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO F 218 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 597 " -0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO E 598 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 598 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 598 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO E 772 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " -0.041 5.00e-02 4.00e+02 ... (remaining 4810 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1962 2.74 - 3.28: 27789 3.28 - 3.82: 45303 3.82 - 4.36: 53508 4.36 - 4.90: 90943 Nonbonded interactions: 219505 Sorted by model distance: nonbonded pdb=" O ILE C 627 " pdb=" OH TYR C 635 " model vdw 2.196 3.040 nonbonded pdb=" OE2 GLU A 628 " pdb=" OG SER A 666 " model vdw 2.242 3.040 nonbonded pdb=" O LEU D 733 " pdb=" OG SER D 736 " model vdw 2.252 3.040 nonbonded pdb=" O LEU A 733 " pdb=" OG SER A 736 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR D 500 " pdb=" OE1 GLU D 503 " model vdw 2.266 3.040 ... (remaining 219500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 9 \ 01)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.600 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.004 0.108 27518 Z= 0.174 Angle : 0.834 13.925 37121 Z= 0.428 Chirality : 0.048 0.341 4233 Planarity : 0.006 0.140 4813 Dihedral : 15.490 153.765 10538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3341 helix: -0.17 (0.12), residues: 1781 sheet: -0.35 (0.25), residues: 400 loop : -0.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 388 TYR 0.032 0.002 TYR A 389 PHE 0.025 0.002 PHE F 394 TRP 0.010 0.001 TRP F 807 HIS 0.012 0.001 HIS B 631 Details of bonding type rmsd covalent geometry : bond 0.00385 (27518) covalent geometry : angle 0.83356 (37121) hydrogen bonds : bond 0.16509 ( 1320) hydrogen bonds : angle 6.81113 ( 3861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 653 ARG cc_start: 0.6700 (mtt90) cc_final: 0.5776 (tpt170) REVERT: A 690 TYR cc_start: 0.7134 (p90) cc_final: 0.6853 (m-80) REVERT: A 727 ILE cc_start: 0.6169 (mt) cc_final: 0.5770 (mt) REVERT: A 747 MET cc_start: 0.5193 (mmp) cc_final: 0.4946 (mmm) REVERT: B 325 LEU cc_start: 0.7696 (mt) cc_final: 0.7193 (mp) REVERT: B 587 ASP cc_start: 0.6259 (m-30) cc_final: 0.5472 (p0) REVERT: B 747 MET cc_start: 0.6789 (mtp) cc_final: 0.6571 (mtp) REVERT: C 638 LEU cc_start: 0.8836 (mt) cc_final: 0.8588 (mp) REVERT: D 815 ASP cc_start: 0.6748 (p0) cc_final: 0.5919 (p0) REVERT: E 510 MET cc_start: 0.6444 (ttp) cc_final: 0.6077 (ttp) REVERT: E 730 MET cc_start: 0.7815 (mmm) cc_final: 0.7583 (mmm) REVERT: F 323 THR cc_start: 0.7035 (m) cc_final: 0.6804 (m) REVERT: F 571 PHE cc_start: 0.6059 (m-80) cc_final: 0.5575 (m-80) REVERT: F 573 ASP cc_start: 0.5473 (p0) cc_final: 0.5220 (p0) REVERT: F 587 ASP cc_start: 0.5963 (m-30) cc_final: 0.5538 (t0) REVERT: F 634 ILE cc_start: 0.7688 (mm) cc_final: 0.7420 (mm) REVERT: F 693 MET cc_start: 0.5982 (mmm) cc_final: 0.5763 (ptm) outliers start: 1 outliers final: 1 residues processed: 420 average time/residue: 0.1649 time to fit residues: 111.7125 Evaluate side-chains 318 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 806 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 343 GLN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 568 ASN D 659 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.152228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118241 restraints weight = 56771.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117500 restraints weight = 35765.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118479 restraints weight = 25315.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.119037 restraints weight = 21561.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119256 restraints weight = 17151.530| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27518 Z= 0.170 Angle : 0.662 8.292 37121 Z= 0.320 Chirality : 0.044 0.222 4233 Planarity : 0.005 0.079 4813 Dihedral : 9.052 164.196 3828 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.09 % Allowed : 9.49 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3341 helix: 0.44 (0.12), residues: 1798 sheet: -0.46 (0.25), residues: 420 loop : 0.28 (0.20), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 615 TYR 0.017 0.002 TYR A 635 PHE 0.028 0.002 PHE C 791 TRP 0.026 0.001 TRP F 807 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00392 (27518) covalent geometry : angle 0.66182 (37121) hydrogen bonds : bond 0.03900 ( 1320) hydrogen bonds : angle 5.19437 ( 3861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 354 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7450 (mt) REVERT: B 501 GLU cc_start: 0.8241 (mp0) cc_final: 0.7701 (pm20) REVERT: B 633 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5778 (mt-10) REVERT: B 701 LEU cc_start: 0.8302 (pp) cc_final: 0.7778 (tt) REVERT: B 747 MET cc_start: 0.6740 (mtp) cc_final: 0.6441 (mtp) REVERT: C 494 ILE cc_start: 0.7999 (mm) cc_final: 0.7669 (mm) REVERT: C 588 ARG cc_start: 0.6700 (mmp-170) cc_final: 0.5927 (mmm-85) REVERT: D 815 ASP cc_start: 0.7302 (p0) cc_final: 0.6739 (p0) REVERT: E 183 MET cc_start: 0.8947 (mpp) cc_final: 0.7917 (mpp) REVERT: E 656 ASP cc_start: 0.8348 (p0) cc_final: 0.8088 (p0) REVERT: F 571 PHE cc_start: 0.5816 (m-80) cc_final: 0.5260 (m-80) REVERT: F 573 ASP cc_start: 0.5172 (p0) cc_final: 0.4870 (p0) REVERT: F 587 ASP cc_start: 0.5621 (m-30) cc_final: 0.5218 (t0) REVERT: F 634 ILE cc_start: 0.7759 (mm) cc_final: 0.7530 (mm) REVERT: F 693 MET cc_start: 0.6267 (mmm) cc_final: 0.6062 (ptt) outliers start: 31 outliers final: 15 residues processed: 366 average time/residue: 0.1801 time to fit residues: 105.9563 Evaluate side-chains 327 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 318 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 515 HIS ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN D 806 ASN E 318 GLN E 343 GLN ** F 640 GLN ** 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 = 0.4196 r_free = 0.4196 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.110966 restraints weight = 57980.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110067 restraints weight = 38556.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.111748 restraints weight = 29032.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112726 restraints weight = 19074.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112894 restraints weight = 17050.731| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 27518 Z= 0.334 Angle : 0.808 9.694 37121 Z= 0.399 Chirality : 0.049 0.204 4233 Planarity : 0.006 0.068 4813 Dihedral : 9.140 178.734 3826 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.43 % Allowed : 13.15 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3341 helix: 0.04 (0.12), residues: 1815 sheet: -0.91 (0.24), residues: 416 loop : 0.00 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 712 TYR 0.018 0.002 TYR C 635 PHE 0.021 0.002 PHE D 595 TRP 0.012 0.002 TRP E 491 HIS 0.008 0.001 HIS E 586 Details of bonding type rmsd covalent geometry : bond 0.00779 (27518) covalent geometry : angle 0.80772 (37121) hydrogen bonds : bond 0.04612 ( 1320) hydrogen bonds : angle 5.40088 ( 3861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5935 (mp) cc_final: 0.5405 (tt) REVERT: B 191 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 385 LEU cc_start: 0.9029 (mm) cc_final: 0.8795 (mp) REVERT: B 389 TYR cc_start: 0.7487 (m-80) cc_final: 0.7101 (m-80) REVERT: B 501 GLU cc_start: 0.8165 (mp0) cc_final: 0.7645 (pm20) REVERT: B 701 LEU cc_start: 0.8324 (pp) cc_final: 0.7844 (tt) REVERT: B 747 MET cc_start: 0.6762 (mtp) cc_final: 0.6482 (mtp) REVERT: C 217 GLU cc_start: 0.7398 (tt0) cc_final: 0.7106 (tt0) REVERT: C 282 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8874 (mt) REVERT: C 494 ILE cc_start: 0.8242 (mm) cc_final: 0.7901 (mm) REVERT: C 617 LYS cc_start: 0.8333 (ptmm) cc_final: 0.8017 (ptmm) REVERT: C 762 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7210 (ttp-170) REVERT: D 282 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7861 (mp) REVERT: D 495 PRO cc_start: 0.8817 (Cg_endo) cc_final: 0.8515 (Cg_exo) REVERT: D 693 MET cc_start: 0.8164 (ttt) cc_final: 0.7962 (ttt) REVERT: D 815 ASP cc_start: 0.7344 (p0) cc_final: 0.6779 (p0) REVERT: E 183 MET cc_start: 0.8917 (mpp) cc_final: 0.8036 (mpp) REVERT: E 187 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.6943 (mp) REVERT: E 329 ARG cc_start: 0.7699 (mtm110) cc_final: 0.6922 (mmm160) REVERT: E 696 LYS cc_start: 0.7777 (tmtt) cc_final: 0.7549 (mmtm) REVERT: F 247 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8997 (tp) REVERT: F 319 THR cc_start: 0.7801 (m) cc_final: 0.7369 (t) REVERT: F 571 PHE cc_start: 0.5909 (m-80) cc_final: 0.5594 (m-80) REVERT: F 573 ASP cc_start: 0.5173 (p0) cc_final: 0.4724 (p0) REVERT: F 617 LYS cc_start: 0.7117 (tppt) cc_final: 0.6261 (mmtm) REVERT: F 634 ILE cc_start: 0.7742 (mm) cc_final: 0.7525 (mm) REVERT: F 693 MET cc_start: 0.6316 (mmm) cc_final: 0.6049 (ptt) REVERT: F 747 MET cc_start: 0.7342 (mmp) cc_final: 0.7138 (mmp) outliers start: 69 outliers final: 44 residues processed: 378 average time/residue: 0.1724 time to fit residues: 107.1270 Evaluate side-chains 351 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 604 TYR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 710 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 264 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 292 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN B 579 GLN C 631 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 631 HIS E 609 GLN ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.150622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117284 restraints weight = 56655.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116161 restraints weight = 34831.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117420 restraints weight = 24088.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.117894 restraints weight = 19575.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.118401 restraints weight = 16513.614| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27518 Z= 0.140 Angle : 0.645 11.670 37121 Z= 0.307 Chirality : 0.044 0.257 4233 Planarity : 0.004 0.070 4813 Dihedral : 8.598 171.420 3826 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.28 % Allowed : 15.75 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3341 helix: 0.45 (0.12), residues: 1810 sheet: -0.78 (0.25), residues: 404 loop : 0.19 (0.21), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 616 TYR 0.010 0.001 TYR C 635 PHE 0.026 0.001 PHE C 791 TRP 0.009 0.001 TRP F 807 HIS 0.023 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00325 (27518) covalent geometry : angle 0.64459 (37121) hydrogen bonds : bond 0.03435 ( 1320) hydrogen bonds : angle 4.95005 ( 3861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5935 (mp) cc_final: 0.5316 (tt) REVERT: A 655 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5625 (t) REVERT: B 389 TYR cc_start: 0.7330 (m-80) cc_final: 0.7044 (m-80) REVERT: B 501 GLU cc_start: 0.8180 (mp0) cc_final: 0.7698 (pm20) REVERT: B 581 ASP cc_start: 0.7551 (t0) cc_final: 0.7203 (m-30) REVERT: B 701 LEU cc_start: 0.8358 (pp) cc_final: 0.7917 (tt) REVERT: B 747 MET cc_start: 0.6509 (mtp) cc_final: 0.6230 (mtp) REVERT: C 410 MET cc_start: 0.8363 (mmp) cc_final: 0.8158 (mmm) REVERT: C 588 ARG cc_start: 0.6435 (mmp-170) cc_final: 0.5717 (mmm-85) REVERT: D 201 MET cc_start: 0.8549 (mmm) cc_final: 0.8346 (mmm) REVERT: D 581 ASP cc_start: 0.7008 (m-30) cc_final: 0.6605 (m-30) REVERT: D 783 ASP cc_start: 0.8097 (m-30) cc_final: 0.7779 (m-30) REVERT: D 815 ASP cc_start: 0.7377 (p0) cc_final: 0.6836 (p0) REVERT: E 183 MET cc_start: 0.8914 (mpp) cc_final: 0.8113 (mpp) REVERT: E 329 ARG cc_start: 0.7676 (mtm110) cc_final: 0.6906 (mmm160) REVERT: E 523 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7448 (p0) REVERT: E 696 LYS cc_start: 0.7570 (tmtt) cc_final: 0.7256 (mmtm) REVERT: E 789 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7824 (mp) REVERT: F 571 PHE cc_start: 0.5890 (m-80) cc_final: 0.5264 (m-80) REVERT: F 573 ASP cc_start: 0.5174 (p0) cc_final: 0.4819 (p0) REVERT: F 617 LYS cc_start: 0.7103 (tppt) cc_final: 0.6300 (mmtm) REVERT: F 693 MET cc_start: 0.6292 (mmm) cc_final: 0.6080 (ptm) outliers start: 65 outliers final: 34 residues processed: 373 average time/residue: 0.1718 time to fit residues: 105.2981 Evaluate side-chains 345 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 710 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 151 optimal weight: 0.4980 chunk 169 optimal weight: 0.0070 chunk 229 optimal weight: 0.0770 chunk 260 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 346 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN D 354 HIS D 631 HIS F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.153918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.120489 restraints weight = 56202.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119316 restraints weight = 35536.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121030 restraints weight = 27056.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.121156 restraints weight = 19796.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121859 restraints weight = 16707.055| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27518 Z= 0.108 Angle : 0.617 10.110 37121 Z= 0.290 Chirality : 0.043 0.278 4233 Planarity : 0.004 0.067 4813 Dihedral : 8.067 168.241 3826 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.04 % Allowed : 16.77 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3341 helix: 0.73 (0.12), residues: 1807 sheet: -0.61 (0.26), residues: 367 loop : 0.30 (0.20), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 616 TYR 0.009 0.001 TYR B 635 PHE 0.026 0.001 PHE D 589 TRP 0.009 0.001 TRP F 807 HIS 0.011 0.001 HIS C 586 Details of bonding type rmsd covalent geometry : bond 0.00238 (27518) covalent geometry : angle 0.61718 (37121) hydrogen bonds : bond 0.03011 ( 1320) hydrogen bonds : angle 4.73078 ( 3861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6943 (tp30) cc_final: 0.6625 (tp30) REVERT: A 539 LEU cc_start: 0.5967 (mp) cc_final: 0.5571 (tt) REVERT: B 501 GLU cc_start: 0.8157 (mp0) cc_final: 0.7712 (pm20) REVERT: B 627 ILE cc_start: 0.8856 (tt) cc_final: 0.7691 (tp) REVERT: B 701 LEU cc_start: 0.8344 (pp) cc_final: 0.7959 (tt) REVERT: B 747 MET cc_start: 0.6434 (mtp) cc_final: 0.6171 (mtp) REVERT: C 494 ILE cc_start: 0.7828 (mm) cc_final: 0.7492 (mm) REVERT: C 588 ARG cc_start: 0.6369 (mmp-170) cc_final: 0.5664 (mmm-85) REVERT: C 753 ASP cc_start: 0.7811 (m-30) cc_final: 0.7601 (m-30) REVERT: D 267 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: D 783 ASP cc_start: 0.8012 (m-30) cc_final: 0.7722 (m-30) REVERT: D 815 ASP cc_start: 0.7336 (p0) cc_final: 0.6793 (p0) REVERT: E 329 ARG cc_start: 0.7653 (mtm110) cc_final: 0.6855 (mmm160) REVERT: E 789 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (mp) REVERT: F 571 PHE cc_start: 0.5918 (m-80) cc_final: 0.5356 (m-80) REVERT: F 573 ASP cc_start: 0.5218 (p0) cc_final: 0.4824 (p0) REVERT: F 617 LYS cc_start: 0.7019 (tppt) cc_final: 0.6213 (mmtm) REVERT: F 693 MET cc_start: 0.6232 (mmm) cc_final: 0.6027 (ptm) outliers start: 58 outliers final: 33 residues processed: 384 average time/residue: 0.1705 time to fit residues: 107.6197 Evaluate side-chains 350 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 315 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 81 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 354 HIS D 806 ASN E 318 GLN F 640 GLN F 651 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.151471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118234 restraints weight = 56750.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.117972 restraints weight = 34651.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.119090 restraints weight = 23932.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.119472 restraints weight = 19689.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.119617 restraints weight = 16571.315| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27518 Z= 0.133 Angle : 0.638 15.070 37121 Z= 0.299 Chirality : 0.044 0.310 4233 Planarity : 0.004 0.064 4813 Dihedral : 7.865 165.528 3826 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.46 % Allowed : 17.40 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3341 helix: 0.76 (0.12), residues: 1814 sheet: -0.70 (0.25), residues: 381 loop : 0.37 (0.20), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 762 TYR 0.011 0.001 TYR A 635 PHE 0.026 0.001 PHE D 589 TRP 0.005 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00311 (27518) covalent geometry : angle 0.63774 (37121) hydrogen bonds : bond 0.03119 ( 1320) hydrogen bonds : angle 4.73543 ( 3861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6872 (tp30) cc_final: 0.6615 (tp30) REVERT: A 323 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 410 MET cc_start: 0.8480 (mmp) cc_final: 0.8263 (mmt) REVERT: B 501 GLU cc_start: 0.8064 (mp0) cc_final: 0.7652 (pm20) REVERT: B 581 ASP cc_start: 0.7500 (t0) cc_final: 0.7069 (m-30) REVERT: B 701 LEU cc_start: 0.8306 (pp) cc_final: 0.7814 (tt) REVERT: B 747 MET cc_start: 0.6599 (mtp) cc_final: 0.6353 (mtp) REVERT: D 815 ASP cc_start: 0.7381 (p0) cc_final: 0.6810 (p0) REVERT: E 183 MET cc_start: 0.8902 (mpp) cc_final: 0.8067 (mpp) REVERT: E 329 ARG cc_start: 0.7702 (mtm110) cc_final: 0.6859 (mmm160) REVERT: E 696 LYS cc_start: 0.7346 (tmtt) cc_final: 0.7107 (mmtt) REVERT: E 789 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7894 (mp) REVERT: F 571 PHE cc_start: 0.5613 (m-80) cc_final: 0.5072 (m-80) REVERT: F 573 ASP cc_start: 0.4823 (p0) cc_final: 0.4453 (p0) REVERT: F 617 LYS cc_start: 0.6920 (tppt) cc_final: 0.6113 (mmtm) outliers start: 70 outliers final: 46 residues processed: 364 average time/residue: 0.1692 time to fit residues: 101.1426 Evaluate side-chains 345 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 643 GLU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 258 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 158 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.152461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.118415 restraints weight = 56635.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.118000 restraints weight = 37109.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119382 restraints weight = 24671.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.119821 restraints weight = 17648.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.119991 restraints weight = 16860.855| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27518 Z= 0.126 Angle : 0.634 13.816 37121 Z= 0.297 Chirality : 0.043 0.327 4233 Planarity : 0.004 0.063 4813 Dihedral : 7.669 161.178 3826 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.53 % Allowed : 18.03 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3341 helix: 0.83 (0.12), residues: 1812 sheet: -0.58 (0.25), residues: 388 loop : 0.43 (0.21), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 653 TYR 0.016 0.001 TYR E 248 PHE 0.025 0.001 PHE D 589 TRP 0.005 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00293 (27518) covalent geometry : angle 0.63444 (37121) hydrogen bonds : bond 0.03067 ( 1320) hydrogen bonds : angle 4.67761 ( 3861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 319 time to evaluate : 1.031 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 275 GLU cc_start: 0.6916 (tp30) cc_final: 0.6626 (tp30) REVERT: A 323 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 539 LEU cc_start: 0.5978 (mp) cc_final: 0.5164 (tt) REVERT: B 501 GLU cc_start: 0.8154 (mp0) cc_final: 0.7715 (pm20) REVERT: B 581 ASP cc_start: 0.7573 (t0) cc_final: 0.7139 (m-30) REVERT: B 701 LEU cc_start: 0.8361 (pp) cc_final: 0.7904 (tt) REVERT: B 747 MET cc_start: 0.6508 (mtp) cc_final: 0.6254 (mtp) REVERT: C 494 ILE cc_start: 0.7855 (mm) cc_final: 0.7546 (mm) REVERT: D 282 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7735 (mp) REVERT: D 690 TYR cc_start: 0.4991 (t80) cc_final: 0.4768 (t80) REVERT: D 815 ASP cc_start: 0.7406 (p0) cc_final: 0.6844 (p0) REVERT: E 329 ARG cc_start: 0.7795 (mtm110) cc_final: 0.6907 (mmm160) REVERT: E 696 LYS cc_start: 0.7398 (tmtt) cc_final: 0.7161 (mmtt) REVERT: E 789 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7903 (mp) REVERT: F 571 PHE cc_start: 0.5783 (m-80) cc_final: 0.5219 (m-80) REVERT: F 573 ASP cc_start: 0.5034 (p0) cc_final: 0.4670 (p0) REVERT: F 617 LYS cc_start: 0.7017 (tppt) cc_final: 0.6199 (mmtm) outliers start: 72 outliers final: 49 residues processed: 369 average time/residue: 0.1759 time to fit residues: 105.1201 Evaluate side-chains 356 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 217 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 315 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 391 ASN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.151213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116444 restraints weight = 57199.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116773 restraints weight = 38724.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118059 restraints weight = 24474.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.118747 restraints weight = 19518.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.118905 restraints weight = 17553.123| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27518 Z= 0.152 Angle : 0.663 13.202 37121 Z= 0.310 Chirality : 0.044 0.316 4233 Planarity : 0.004 0.063 4813 Dihedral : 7.639 160.627 3826 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.57 % Allowed : 18.70 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3341 helix: 0.83 (0.12), residues: 1818 sheet: -0.63 (0.25), residues: 393 loop : 0.45 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 340 TYR 0.015 0.001 TYR A 635 PHE 0.025 0.001 PHE D 589 TRP 0.004 0.001 TRP E 491 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00357 (27518) covalent geometry : angle 0.66336 (37121) hydrogen bonds : bond 0.03182 ( 1320) hydrogen bonds : angle 4.71226 ( 3861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 318 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7374 (m) cc_final: 0.7081 (m) REVERT: A 275 GLU cc_start: 0.6927 (tp30) cc_final: 0.6638 (tp30) REVERT: A 323 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 539 LEU cc_start: 0.5902 (mp) cc_final: 0.5268 (tt) REVERT: B 501 GLU cc_start: 0.8144 (mp0) cc_final: 0.7717 (pm20) REVERT: B 581 ASP cc_start: 0.7559 (t0) cc_final: 0.7107 (m-30) REVERT: B 701 LEU cc_start: 0.8361 (pp) cc_final: 0.7905 (tt) REVERT: B 747 MET cc_start: 0.6398 (mtp) cc_final: 0.6172 (mtp) REVERT: D 282 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7742 (mp) REVERT: D 510 MET cc_start: 0.7485 (ppp) cc_final: 0.7118 (ppp) REVERT: D 815 ASP cc_start: 0.7299 (p0) cc_final: 0.6741 (p0) REVERT: E 183 MET cc_start: 0.8880 (mpp) cc_final: 0.8047 (mpp) REVERT: E 187 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7644 (mp) REVERT: E 329 ARG cc_start: 0.7761 (mtm110) cc_final: 0.6932 (mmm160) REVERT: E 696 LYS cc_start: 0.7432 (tmtt) cc_final: 0.7206 (mmtt) REVERT: E 789 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7932 (mp) REVERT: F 571 PHE cc_start: 0.5877 (m-80) cc_final: 0.5298 (m-80) REVERT: F 573 ASP cc_start: 0.5121 (p0) cc_final: 0.4742 (p0) REVERT: F 617 LYS cc_start: 0.7097 (tppt) cc_final: 0.6246 (mmtm) REVERT: F 662 LEU cc_start: 0.8223 (mm) cc_final: 0.8000 (mm) outliers start: 73 outliers final: 57 residues processed: 367 average time/residue: 0.1707 time to fit residues: 101.5212 Evaluate side-chains 359 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 693 MET Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 306 optimal weight: 0.0770 chunk 266 optimal weight: 0.4980 chunk 153 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 92 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 ASN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN C 806 ASN F 720 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.152030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118344 restraints weight = 56650.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.118223 restraints weight = 36036.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.118898 restraints weight = 24064.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119382 restraints weight = 21596.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.119643 restraints weight = 17754.321| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27518 Z= 0.111 Angle : 0.656 16.437 37121 Z= 0.304 Chirality : 0.043 0.309 4233 Planarity : 0.004 0.061 4813 Dihedral : 7.433 158.395 3826 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.32 % Allowed : 19.16 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3341 helix: 0.92 (0.12), residues: 1821 sheet: -0.49 (0.25), residues: 402 loop : 0.51 (0.21), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.009 0.001 TYR D 690 PHE 0.027 0.001 PHE D 589 TRP 0.007 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00255 (27518) covalent geometry : angle 0.65634 (37121) hydrogen bonds : bond 0.02934 ( 1320) hydrogen bonds : angle 4.65846 ( 3861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 1.510 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 223 THR cc_start: 0.7352 (m) cc_final: 0.7066 (m) REVERT: A 323 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8495 (p) REVERT: A 539 LEU cc_start: 0.5945 (mp) cc_final: 0.5253 (tt) REVERT: A 693 MET cc_start: 0.3009 (tpt) cc_final: 0.2616 (mtm) REVERT: B 501 GLU cc_start: 0.8154 (mp0) cc_final: 0.7713 (pm20) REVERT: B 627 ILE cc_start: 0.8819 (tt) cc_final: 0.8448 (tp) REVERT: B 701 LEU cc_start: 0.8401 (pp) cc_final: 0.7970 (tt) REVERT: B 747 MET cc_start: 0.6478 (mtp) cc_final: 0.6256 (mtp) REVERT: C 494 ILE cc_start: 0.7884 (mm) cc_final: 0.7592 (mm) REVERT: D 510 MET cc_start: 0.7388 (ppp) cc_final: 0.7036 (ppp) REVERT: D 640 GLN cc_start: 0.8396 (pm20) cc_final: 0.8167 (pm20) REVERT: D 783 ASP cc_start: 0.8083 (m-30) cc_final: 0.7746 (m-30) REVERT: D 815 ASP cc_start: 0.7390 (p0) cc_final: 0.6635 (p0) REVERT: E 329 ARG cc_start: 0.7757 (mtm110) cc_final: 0.6866 (mmm160) REVERT: E 696 LYS cc_start: 0.7448 (tmtt) cc_final: 0.7214 (mmtt) REVERT: E 703 LYS cc_start: 0.9289 (mptt) cc_final: 0.9026 (mmtm) REVERT: E 789 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7864 (mp) REVERT: F 571 PHE cc_start: 0.5697 (m-80) cc_final: 0.5122 (m-80) REVERT: F 573 ASP cc_start: 0.4910 (p0) cc_final: 0.4590 (p0) REVERT: F 617 LYS cc_start: 0.7004 (tppt) cc_final: 0.6151 (mmtm) outliers start: 66 outliers final: 51 residues processed: 373 average time/residue: 0.1643 time to fit residues: 99.1849 Evaluate side-chains 365 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 114 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 236 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 173 optimal weight: 0.1980 chunk 220 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.151566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118543 restraints weight = 56926.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.118379 restraints weight = 34860.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.119329 restraints weight = 24373.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.119806 restraints weight = 19118.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120013 restraints weight = 16896.334| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27518 Z= 0.120 Angle : 0.659 20.038 37121 Z= 0.307 Chirality : 0.043 0.214 4233 Planarity : 0.004 0.062 4813 Dihedral : 7.353 157.282 3826 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.04 % Allowed : 19.58 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3341 helix: 0.93 (0.12), residues: 1822 sheet: -0.50 (0.25), residues: 416 loop : 0.57 (0.21), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 340 TYR 0.015 0.001 TYR A 635 PHE 0.026 0.001 PHE D 589 TRP 0.007 0.001 TRP C 807 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00279 (27518) covalent geometry : angle 0.65852 (37121) hydrogen bonds : bond 0.02959 ( 1320) hydrogen bonds : angle 4.65856 ( 3861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 1.115 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 223 THR cc_start: 0.7420 (m) cc_final: 0.7120 (m) REVERT: A 323 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 539 LEU cc_start: 0.5819 (mp) cc_final: 0.5226 (tt) REVERT: A 693 MET cc_start: 0.2946 (tpt) cc_final: 0.2496 (mtm) REVERT: B 501 GLU cc_start: 0.8019 (mp0) cc_final: 0.7636 (pm20) REVERT: B 627 ILE cc_start: 0.8843 (tt) cc_final: 0.8482 (tp) REVERT: B 701 LEU cc_start: 0.8300 (pp) cc_final: 0.7844 (tt) REVERT: B 747 MET cc_start: 0.6534 (mtp) cc_final: 0.6326 (mtp) REVERT: C 494 ILE cc_start: 0.7871 (mm) cc_final: 0.7584 (mm) REVERT: D 510 MET cc_start: 0.7427 (ppp) cc_final: 0.7120 (ppp) REVERT: D 640 GLN cc_start: 0.8374 (pm20) cc_final: 0.8163 (pm20) REVERT: D 693 MET cc_start: 0.7957 (ttt) cc_final: 0.7609 (ttt) REVERT: D 815 ASP cc_start: 0.7291 (p0) cc_final: 0.6720 (p0) REVERT: E 329 ARG cc_start: 0.7735 (mtm110) cc_final: 0.6871 (mmm160) REVERT: E 703 LYS cc_start: 0.9265 (mptt) cc_final: 0.9036 (mmtm) REVERT: E 789 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7922 (mp) REVERT: F 571 PHE cc_start: 0.5444 (m-80) cc_final: 0.4908 (m-80) REVERT: F 573 ASP cc_start: 0.4648 (p0) cc_final: 0.4355 (p0) REVERT: F 617 LYS cc_start: 0.6955 (tppt) cc_final: 0.6087 (mmtm) outliers start: 58 outliers final: 49 residues processed: 355 average time/residue: 0.1732 time to fit residues: 99.4402 Evaluate side-chains 357 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 789 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 258 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 92 optimal weight: 0.0370 chunk 133 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 chunk 237 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN D 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.150753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115352 restraints weight = 56812.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116421 restraints weight = 36448.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.118142 restraints weight = 23298.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.118698 restraints weight = 17016.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.118868 restraints weight = 15321.544| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27518 Z= 0.118 Angle : 0.681 21.783 37121 Z= 0.317 Chirality : 0.044 0.250 4233 Planarity : 0.004 0.062 4813 Dihedral : 7.223 153.737 3826 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.97 % Allowed : 19.86 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3341 helix: 0.93 (0.12), residues: 1826 sheet: -0.44 (0.25), residues: 403 loop : 0.57 (0.21), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 724 TYR 0.010 0.001 TYR E 248 PHE 0.027 0.001 PHE D 589 TRP 0.006 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00274 (27518) covalent geometry : angle 0.68075 (37121) hydrogen bonds : bond 0.02949 ( 1320) hydrogen bonds : angle 4.64858 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.62 seconds wall clock time: 76 minutes 54.26 seconds (4614.26 seconds total)