Starting phenix.real_space_refine on Wed Nov 19 22:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djv_7943/11_2025/6djv_7943.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 891 atoms to isotropic. 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 34 5.49 5 S 64 5.16 5 C 16985 2.51 5 N 4966 2.21 5 O 5269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4649 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4657 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 4678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4678 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4289 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.27, per 1000 atoms: 0.27 Number of scatterers: 27318 At special positions: 0 Unit cell: (138.546, 147.138, 134.25, 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 64 16.00 P 34 15.00 O 5269 8.00 N 4966 7.00 C 16985 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 29 sheets defined 48.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 159 through 165 removed outlier: 4.132A pdb=" N LYS A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.706A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.708A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.783A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.598A pdb=" N LEU A 232 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 233 " --> pdb=" O GLU A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 233' Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 317 through 324 removed outlier: 3.640A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.805A pdb=" N ARG A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.729A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.609A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.992A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 444 through 469 Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.760A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.538A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.822A pdb=" N ASP A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.538A pdb=" N ALA A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.759A pdb=" N VAL A 645 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 649 " --> pdb=" O ALA A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.840A pdb=" N ARG A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.511A pdb=" N ILE A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.853A pdb=" N VAL A 762 " --> pdb=" O PRO A 758 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 removed outlier: 3.884A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 796 " --> pdb=" O TRP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.806A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.587A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.510A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.519A pdb=" N LEU B 232 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.617A pdb=" N ALA B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.569A pdb=" N SER B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 300 through 307 removed outlier: 4.196A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 removed outlier: 3.888A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 removed outlier: 4.011A pdb=" N ALA B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.447A pdb=" N ARG B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.984A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 removed outlier: 4.249A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 378 removed outlier: 3.692A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.916A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 Processing helix chain 'B' and resid 444 through 469 Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.604A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.069A pdb=" N ARG B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.545A pdb=" N LYS B 570 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 571' Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.693A pdb=" N VAL B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 648 removed outlier: 3.714A pdb=" N ARG B 647 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.642A pdb=" N VAL B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 4.436A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 734 Processing helix chain 'B' and resid 734 through 739 removed outlier: 4.009A pdb=" N THR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 776 removed outlier: 4.423A pdb=" N ARG B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 797 removed outlier: 3.779A pdb=" N LEU B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 815 removed outlier: 4.733A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 825 removed outlier: 3.877A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.660A pdb=" N GLU C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.762A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 4.031A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.679A pdb=" N GLU C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 305 removed outlier: 4.106A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.973A pdb=" N HIS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 328 removed outlier: 4.074A pdb=" N ALA C 328 " --> pdb=" O GLU C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.537A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 367 through 378 removed outlier: 3.756A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.736A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 431 Processing helix chain 'C' and resid 444 through 469 Processing helix chain 'C' and resid 534 through 544 removed outlier: 3.746A pdb=" N ILE C 538 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.501A pdb=" N LYS C 570 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 571 " --> pdb=" O LEU C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 571' Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.550A pdb=" N VAL C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 620 removed outlier: 3.863A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 648 removed outlier: 4.042A pdb=" N VAL C 645 " --> pdb=" O LYS C 642 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.597A pdb=" N VAL C 668 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 739 removed outlier: 3.934A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 757 through 776 removed outlier: 3.867A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 786 through 796 removed outlier: 3.830A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 815 removed outlier: 4.156A pdb=" N GLN C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 removed outlier: 3.701A pdb=" N LEU C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.580A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.723A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.908A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.868A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.822A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.664A pdb=" N ARG D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 367 through 382 removed outlier: 3.851A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 382 " --> pdb=" O SER D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 407 removed outlier: 4.294A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.501A pdb=" N ASP D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 Processing helix chain 'D' and resid 564 through 569 Processing helix chain 'D' and resid 579 through 591 removed outlier: 3.591A pdb=" N ALA D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 586 " --> pdb=" O VAL D 582 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG D 588 " --> pdb=" O ASP D 584 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 591 " --> pdb=" O ARG D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 624 removed outlier: 3.713A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 649 removed outlier: 3.556A pdb=" N THR D 644 " --> pdb=" O GLU D 641 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 649 " --> pdb=" O ALA D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 4.156A pdb=" N VAL D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 691 through 696 removed outlier: 3.745A pdb=" N VAL D 695 " --> pdb=" O VAL D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 739 removed outlier: 3.539A pdb=" N VAL D 735 " --> pdb=" O VAL D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 776 removed outlier: 3.711A pdb=" N ILE D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP D 766 " --> pdb=" O VAL D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 806 through 825 removed outlier: 4.303A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.504A pdb=" N ARG E 173 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 211 through 226 removed outlier: 3.782A pdb=" N ALA E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.777A pdb=" N ALA E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.652A pdb=" N ARG E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 317 through 321' Processing helix chain 'E' and resid 343 through 354 Processing helix chain 'E' and resid 367 through 382 removed outlier: 4.026A pdb=" N LEU E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE E 382 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 391 removed outlier: 3.825A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 407 removed outlier: 3.625A pdb=" N MET E 404 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 405 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 547 removed outlier: 4.094A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 Processing helix chain 'E' and resid 587 through 592 removed outlier: 3.740A pdb=" N ARG E 590 " --> pdb=" O ARG E 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 591 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY E 592 " --> pdb=" O SER E 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 587 through 592' Processing helix chain 'E' and resid 614 through 625 removed outlier: 3.564A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 649 removed outlier: 3.605A pdb=" N ILE E 649 " --> pdb=" O ALA E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 668 Processing helix chain 'E' and resid 680 through 684 removed outlier: 3.974A pdb=" N LYS E 683 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 696 removed outlier: 3.682A pdb=" N GLN E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 695 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 696 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 739 removed outlier: 3.712A pdb=" N LEU E 732 " --> pdb=" O ALA E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 747 removed outlier: 3.951A pdb=" N ASN E 745 " --> pdb=" O PRO E 741 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 746 " --> pdb=" O GLU E 742 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 747 " --> pdb=" O PHE E 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 747' Processing helix chain 'E' and resid 760 through 774 removed outlier: 4.223A pdb=" N ILE E 764 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 765 " --> pdb=" O LEU E 761 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 778 removed outlier: 4.121A pdb=" N GLN E 778 " --> pdb=" O ARG E 775 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 775 through 778' Processing helix chain 'E' and resid 786 through 796 removed outlier: 4.122A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 826 removed outlier: 4.154A pdb=" N GLN E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE E 815 " --> pdb=" O VAL E 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.804A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 226 removed outlier: 3.993A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.688A pdb=" N ARG F 233 " --> pdb=" O GLU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 267 removed outlier: 3.519A pdb=" N GLU F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 283 removed outlier: 3.692A pdb=" N ILE F 283 " --> pdb=" O LEU F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 300 through 305 removed outlier: 4.380A pdb=" N ALA F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 326 removed outlier: 3.965A pdb=" N LYS F 326 " --> pdb=" O HIS F 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 323 through 326' Processing helix chain 'F' and resid 327 through 332 removed outlier: 4.252A pdb=" N GLU F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 327 through 332' Processing helix chain 'F' and resid 343 through 354 Processing helix chain 'F' and resid 356 through 362 removed outlier: 3.704A pdb=" N VAL F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 378 removed outlier: 3.975A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 406 removed outlier: 4.145A pdb=" N LEU F 394 " --> pdb=" O LYS F 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE F 406 " --> pdb=" O LEU F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 543 removed outlier: 3.548A pdb=" N ILE F 538 " --> pdb=" O GLY F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 Processing helix chain 'F' and resid 567 through 571 removed outlier: 3.604A pdb=" N LYS F 570 " --> pdb=" O GLU F 567 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG F 571 " --> pdb=" O LEU F 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 567 through 571' Processing helix chain 'F' and resid 575 through 591 removed outlier: 3.551A pdb=" N ALA F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 590 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 591 " --> pdb=" O ARG F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 625 removed outlier: 3.824A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.594A pdb=" N THR F 644 " --> pdb=" O GLU F 641 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 671 removed outlier: 3.919A pdb=" N ALA F 667 " --> pdb=" O GLN F 663 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL F 668 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG F 671 " --> pdb=" O ALA F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 694 removed outlier: 3.747A pdb=" N VAL F 691 " --> pdb=" O ASP F 687 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 737 removed outlier: 3.511A pdb=" N LEU F 732 " --> pdb=" O ALA F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 776 removed outlier: 3.986A pdb=" N ILE F 764 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 786 through 796 removed outlier: 3.858A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 804 through 824 removed outlier: 3.885A pdb=" N ARG F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG F 809 " --> pdb=" O ARG F 805 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 812 " --> pdb=" O ARG F 808 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 816 " --> pdb=" O GLN F 812 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.197A pdb=" N LEU A 204 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 203 " --> pdb=" O VAL A 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 239 removed outlier: 6.713A pdb=" N VAL A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 631 through 635 removed outlier: 4.014A pdb=" N ILE A 634 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 679 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 676 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR A 719 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A 678 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N LEU A 751 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N MET A 604 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 701 removed outlier: 3.540A pdb=" N LEU A 701 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 785 removed outlier: 3.559A pdb=" N VAL A 836 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 837 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 236 through 239 removed outlier: 6.307A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG B 310 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 314 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR B 315 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 204 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 366 removed outlier: 7.384A pdb=" N ARG B 365 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 632 through 635 removed outlier: 4.417A pdb=" N ILE B 634 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 679 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY B 601 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU B 718 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 603 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LEU B 751 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET B 604 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 700 through 701 removed outlier: 3.609A pdb=" N LEU B 701 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 782 through 785 removed outlier: 6.788A pdb=" N GLN B 782 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 836 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN B 784 " --> pdb=" O VAL B 836 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 276 through 278 removed outlier: 4.157A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY C 206 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 203 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.298A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.582A pdb=" N LEU C 677 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 634 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 679 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY C 601 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU C 718 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE C 603 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 700 through 702 Processing sheet with id=AB6, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.726A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 167 Processing sheet with id=AB8, first strand: chain 'D' and resid 204 through 206 removed outlier: 6.681A pdb=" N ILE D 205 " --> pdb=" O VAL D 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.866A pdb=" N ALA D 314 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 632 through 635 removed outlier: 3.573A pdb=" N ASP D 679 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 605 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 700 through 701 Processing sheet with id=AC3, first strand: chain 'D' and resid 783 through 784 Processing sheet with id=AC4, first strand: chain 'E' and resid 236 through 237 removed outlier: 6.238A pdb=" N THR E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE E 276 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 312 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR E 315 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 204 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 631 through 635 removed outlier: 6.362A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP E 679 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE E 634 " --> pdb=" O ASP E 679 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 702 Processing sheet with id=AC7, first strand: chain 'F' and resid 236 through 238 removed outlier: 8.901A pdb=" N VAL F 312 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR F 275 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ALA F 314 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE F 277 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N THR F 316 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY F 206 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 632 through 635 removed outlier: 6.907A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL F 676 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR F 719 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE F 678 " --> pdb=" O THR F 719 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 601 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU F 718 " --> pdb=" O GLY F 601 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE F 603 " --> pdb=" O LEU F 718 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 700 through 702 Processing sheet with id=AD1, first strand: chain 'F' and resid 783 through 784 Processing sheet with id=AD2, first strand: chain 'F' and resid 837 through 839 removed outlier: 3.911A pdb=" N SER F 839 " --> pdb=" O ALA F 842 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10804 1.39 - 1.56: 16734 1.56 - 1.73: 38 1.73 - 1.90: 108 1.90 - 2.08: 10 Bond restraints: 27694 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.27e+01 bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.15e+01 bond pdb=" C5 AGS D 901 " pdb=" C6 AGS D 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" PG AGS F 901 " pdb=" S1G AGS F 901 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 27689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 36841 3.48 - 6.96: 524 6.96 - 10.43: 99 10.43 - 13.91: 10 13.91 - 17.39: 3 Bond angle restraints: 37477 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N3 AGS D 901 " ideal model delta sigma weight residual 126.80 118.71 8.09 7.41e-01 1.82e+00 1.19e+02 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 106.56 4.17 4.52e-01 4.89e+00 8.50e+01 angle pdb=" C SER C 594 " pdb=" N ASP C 595 " pdb=" CA ASP C 595 " ideal model delta sigma weight residual 120.94 138.33 -17.39 1.90e+00 2.77e-01 8.38e+01 angle pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 110.73 106.60 4.13 4.52e-01 4.89e+00 8.33e+01 ... (remaining 37472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 16647 32.67 - 65.33: 372 65.33 - 98.00: 27 98.00 - 130.67: 3 130.67 - 163.34: 3 Dihedral angle restraints: 17052 sinusoidal: 7016 harmonic: 10036 Sorted by residual: dihedral pdb=" CA SER C 839 " pdb=" C SER C 839 " pdb=" N PRO C 840 " pdb=" CA PRO C 840 " ideal model delta harmonic sigma weight residual 180.00 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+01 dihedral pdb=" CA SER E 839 " pdb=" C SER E 839 " pdb=" N PRO E 840 " pdb=" CA PRO E 840 " ideal model delta harmonic sigma weight residual -180.00 -135.46 -44.54 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA LEU C 387 " pdb=" C LEU C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 135.83 44.17 0 5.00e+00 4.00e-02 7.80e+01 ... (remaining 17049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3696 0.082 - 0.164: 572 0.164 - 0.245: 27 0.245 - 0.327: 3 0.327 - 0.409: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ARG E 805 " pdb=" N ARG E 805 " pdb=" C ARG E 805 " pdb=" CB ARG E 805 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB VAL F 180 " pdb=" CA VAL F 180 " pdb=" CG1 VAL F 180 " pdb=" CG2 VAL F 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4297 not shown) Planarity restraints: 4894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 409 " 0.094 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO B 410 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 387 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 388 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 387 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO D 388 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO D 388 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 388 " -0.066 5.00e-02 4.00e+02 ... (remaining 4891 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 137 2.51 - 3.11: 18788 3.11 - 3.71: 39433 3.71 - 4.30: 52373 4.30 - 4.90: 87227 Nonbonded interactions: 197958 Sorted by model distance: nonbonded pdb=" O TRP F 545 " pdb=" N GLY F 547 " model vdw 1.913 3.120 nonbonded pdb=" NH1 ARG B 418 " pdb=" OD1 ASP C 184 " model vdw 1.981 3.120 nonbonded pdb=" O LYS B 301 " pdb=" NH1 ARG B 333 " model vdw 1.986 3.120 nonbonded pdb=" NZ LYS E 199 " pdb=" O ARG E 332 " model vdw 2.082 3.120 nonbonded pdb=" O GLU B 412 " pdb=" N GLU B 415 " model vdw 2.148 3.120 ... (remaining 197953 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 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'B' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'C' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'D' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'E' and resid 159 through 845) selection = (chain 'F' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 845)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.510 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.126 27694 Z= 0.318 Angle : 1.110 17.391 37477 Z= 0.617 Chirality : 0.056 0.409 4300 Planarity : 0.009 0.146 4894 Dihedral : 13.453 163.336 10588 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.49 % Favored : 87.08 % Rotamer: Outliers : 0.72 % Allowed : 5.77 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.34 % Twisted General : 0.12 % 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: -4.95 (0.11), residues: 3484 helix: -3.40 (0.09), residues: 1474 sheet: -2.81 (0.24), residues: 352 loop : -3.23 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 670 TYR 0.026 0.003 TYR E 655 PHE 0.030 0.003 PHE B 753 TRP 0.043 0.004 TRP B 545 HIS 0.011 0.002 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00639 (27694) covalent geometry : angle 1.11036 (37477) hydrogen bonds : bond 0.19974 ( 892) hydrogen bonds : angle 7.71337 ( 2526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 762 time to evaluate : 1.122 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 265 ASP cc_start: 0.7271 (t0) cc_final: 0.7019 (t0) REVERT: A 554 LEU cc_start: 0.7984 (mt) cc_final: 0.7651 (mp) REVERT: A 597 ASN cc_start: 0.8019 (p0) cc_final: 0.7780 (p0) REVERT: B 277 ILE cc_start: 0.9268 (mt) cc_final: 0.9006 (tt) REVERT: B 318 ASP cc_start: 0.8293 (p0) cc_final: 0.8043 (p0) REVERT: B 426 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5594 (mm-30) REVERT: B 697 ASP cc_start: 0.7642 (t70) cc_final: 0.7403 (t0) REVERT: C 442 LEU cc_start: 0.1934 (OUTLIER) cc_final: 0.1692 (mt) REVERT: C 732 LEU cc_start: 0.8906 (tm) cc_final: 0.8673 (tp) REVERT: D 257 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7167 (tp30) REVERT: D 584 ASP cc_start: 0.7163 (m-30) cc_final: 0.6767 (t0) REVERT: D 631 MET cc_start: 0.7014 (pp-130) cc_final: 0.6645 (pp-130) REVERT: E 205 ILE cc_start: 0.9023 (mt) cc_final: 0.8816 (mt) REVERT: E 319 GLU cc_start: 0.7592 (mp0) cc_final: 0.7142 (mp0) REVERT: E 389 ASP cc_start: 0.8363 (p0) cc_final: 0.7968 (t70) REVERT: F 171 ARG cc_start: 0.7068 (mtp85) cc_final: 0.6507 (mtm180) REVERT: F 213 THR cc_start: 0.7418 (m) cc_final: 0.7154 (m) REVERT: F 244 SER cc_start: 0.7751 (p) cc_final: 0.7400 (t) REVERT: F 685 HIS cc_start: 0.8615 (t70) cc_final: 0.8315 (t-90) REVERT: F 756 LEU cc_start: 0.8594 (mt) cc_final: 0.8372 (mt) outliers start: 20 outliers final: 10 residues processed: 781 average time/residue: 0.2546 time to fit residues: 284.9225 Evaluate side-chains 355 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 343 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain F residue 545 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 335 GLN A 361 HIS A 643 HIS B 643 HIS ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 ASN C 361 HIS C 575 GLN C 643 HIS ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN D 361 HIS D 795 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 HIS F 643 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS F 745 ASN ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096162 restraints weight = 57114.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098127 restraints weight = 36393.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099540 restraints weight = 26516.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100611 restraints weight = 21492.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101153 restraints weight = 18635.469| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27694 Z= 0.147 Angle : 0.744 15.728 37477 Z= 0.373 Chirality : 0.045 0.215 4300 Planarity : 0.006 0.098 4894 Dihedral : 11.632 147.546 4120 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.82 % Favored : 89.01 % Rotamer: Outliers : 2.69 % Allowed : 12.69 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.93 % Twisted General : 0.06 % 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: -3.51 (0.13), residues: 3484 helix: -1.83 (0.12), residues: 1528 sheet: -2.15 (0.28), residues: 308 loop : -2.84 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 352 TYR 0.025 0.002 TYR F 338 PHE 0.023 0.002 PHE D 625 TRP 0.021 0.002 TRP D 792 HIS 0.005 0.001 HIS C 829 Details of bonding type rmsd covalent geometry : bond 0.00321 (27694) covalent geometry : angle 0.74388 (37477) hydrogen bonds : bond 0.04455 ( 892) hydrogen bonds : angle 5.09296 ( 2526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 410 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: B 388 PRO cc_start: 0.8865 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: B 680 GLU cc_start: 0.7760 (mp0) cc_final: 0.7307 (mm-30) REVERT: B 703 ASP cc_start: 0.8738 (p0) cc_final: 0.8221 (p0) REVERT: C 623 PHE cc_start: 0.7106 (p90) cc_final: 0.6854 (p90) REVERT: C 732 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8739 (tp) REVERT: D 257 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7498 (tp30) REVERT: D 584 ASP cc_start: 0.7772 (m-30) cc_final: 0.7053 (t0) REVERT: D 718 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8665 (pp) REVERT: E 200 ASN cc_start: 0.8714 (p0) cc_final: 0.8227 (p0) REVERT: E 311 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8078 (tm) REVERT: E 390 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7638 (mtpp) REVERT: F 171 ARG cc_start: 0.6756 (mtp85) cc_final: 0.6424 (mtp180) REVERT: F 244 SER cc_start: 0.7913 (p) cc_final: 0.7663 (t) REVERT: F 692 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8680 (tt) REVERT: F 732 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8916 (tm) outliers start: 75 outliers final: 35 residues processed: 463 average time/residue: 0.1890 time to fit residues: 138.2402 Evaluate side-chains 354 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 586 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 693 LEU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 78 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS B 597 ASN B 685 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS F 705 HIS F 771 GLN F 784 GLN F 827 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096082 restraints weight = 57144.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098286 restraints weight = 36518.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099844 restraints weight = 26781.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100665 restraints weight = 21704.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101572 restraints weight = 19016.673| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27694 Z= 0.122 Angle : 0.685 13.173 37477 Z= 0.339 Chirality : 0.043 0.223 4300 Planarity : 0.006 0.107 4894 Dihedral : 11.030 157.647 4104 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.07 % Favored : 89.75 % Rotamer: Outliers : 3.55 % Allowed : 14.34 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.23 % Twisted General : 0.03 % 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: -2.68 (0.14), residues: 3484 helix: -0.95 (0.13), residues: 1540 sheet: -1.95 (0.29), residues: 301 loop : -2.57 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 171 TYR 0.019 0.001 TYR F 338 PHE 0.015 0.001 PHE B 386 TRP 0.016 0.001 TRP D 792 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00266 (27694) covalent geometry : angle 0.68530 (37477) hydrogen bonds : bond 0.03660 ( 892) hydrogen bonds : angle 4.58992 ( 2526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 353 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: B 254 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6839 (mt-10) REVERT: C 732 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8663 (tp) REVERT: C 769 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 817 ASP cc_start: 0.7063 (p0) cc_final: 0.6697 (p0) REVERT: D 257 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7553 (tp30) REVERT: D 564 MET cc_start: 0.7747 (ptm) cc_final: 0.7437 (ptp) REVERT: D 584 ASP cc_start: 0.7718 (m-30) cc_final: 0.7026 (t0) REVERT: E 311 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8155 (tm) REVERT: E 390 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7638 (mtpp) REVERT: F 171 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6355 (mtm180) REVERT: F 371 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (mt) REVERT: F 669 ARG cc_start: 0.8396 (ptm160) cc_final: 0.8003 (ttp-110) REVERT: F 817 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7562 (p0) outliers start: 99 outliers final: 49 residues processed: 434 average time/residue: 0.1806 time to fit residues: 126.4176 Evaluate side-chains 346 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 629 ARG Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 659 GLU Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 362 HIS E 685 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090854 restraints weight = 58167.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.092462 restraints weight = 39369.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093937 restraints weight = 27919.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094271 restraints weight = 23304.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.094328 restraints weight = 20224.179| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 27694 Z= 0.323 Angle : 0.857 13.157 37477 Z= 0.424 Chirality : 0.050 0.231 4300 Planarity : 0.007 0.111 4894 Dihedral : 11.251 172.051 4101 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.88 % Favored : 87.92 % Rotamer: Outliers : 4.48 % Allowed : 15.84 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.52 % Twisted General : 0.03 % 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: -2.64 (0.14), residues: 3484 helix: -0.78 (0.13), residues: 1562 sheet: -2.23 (0.26), residues: 349 loop : -2.65 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 171 TYR 0.021 0.002 TYR E 658 PHE 0.037 0.003 PHE B 605 TRP 0.026 0.002 TRP C 545 HIS 0.008 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00748 (27694) covalent geometry : angle 0.85683 (37477) hydrogen bonds : bond 0.04809 ( 892) hydrogen bonds : angle 4.88912 ( 2526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 281 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: B 827 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: C 164 TYR cc_start: 0.8069 (m-80) cc_final: 0.7781 (m-80) REVERT: C 769 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8018 (mm) REVERT: C 822 MET cc_start: 0.8237 (ppp) cc_final: 0.7800 (ppp) REVERT: D 257 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7772 (tp30) REVERT: D 264 ASP cc_start: 0.8124 (t0) cc_final: 0.7875 (t0) REVERT: D 564 MET cc_start: 0.7816 (ptm) cc_final: 0.7555 (ptm) REVERT: D 584 ASP cc_start: 0.7818 (m-30) cc_final: 0.7041 (t0) REVERT: D 718 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8874 (pp) REVERT: E 181 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8303 (pt) REVERT: E 221 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: E 245 MET cc_start: 0.6165 (mpp) cc_final: 0.5896 (mpp) REVERT: E 311 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8286 (tm) REVERT: E 390 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7621 (mtpp) REVERT: F 171 ARG cc_start: 0.6663 (mtp85) cc_final: 0.6143 (mtm180) REVERT: F 371 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8161 (mt) REVERT: F 824 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8895 (pp) outliers start: 125 outliers final: 74 residues processed: 386 average time/residue: 0.1719 time to fit residues: 107.9080 Evaluate side-chains 329 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 586 VAL Chi-restraints excluded: chain F residue 604 MET Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 149 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 260 optimal weight: 0.3980 chunk 313 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN C 201 ASN C 721 ASN D 201 ASN E 221 GLN F 663 GLN F 705 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094377 restraints weight = 56943.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096102 restraints weight = 37555.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098049 restraints weight = 25697.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098080 restraints weight = 21670.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098201 restraints weight = 19147.633| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27694 Z= 0.129 Angle : 0.694 14.301 37477 Z= 0.338 Chirality : 0.044 0.239 4300 Planarity : 0.005 0.100 4894 Dihedral : 10.592 175.087 4101 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.79 % Favored : 90.04 % Rotamer: Outliers : 4.01 % Allowed : 16.95 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -2.19 (0.14), residues: 3484 helix: -0.37 (0.14), residues: 1550 sheet: -2.01 (0.27), residues: 341 loop : -2.44 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 629 TYR 0.022 0.001 TYR E 658 PHE 0.021 0.002 PHE A 623 TRP 0.020 0.002 TRP E 545 HIS 0.007 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00289 (27694) covalent geometry : angle 0.69446 (37477) hydrogen bonds : bond 0.03551 ( 892) hydrogen bonds : angle 4.46828 ( 2526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: A 769 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9050 (mm) REVERT: B 217 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: B 827 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: C 164 TYR cc_start: 0.7891 (m-80) cc_final: 0.7651 (m-80) REVERT: C 604 MET cc_start: 0.8459 (ttp) cc_final: 0.8145 (ptm) REVERT: C 732 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 769 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7980 (mm) REVERT: C 822 MET cc_start: 0.8101 (ppp) cc_final: 0.7828 (ppp) REVERT: D 257 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7728 (tp30) REVERT: D 584 ASP cc_start: 0.7780 (m-30) cc_final: 0.7117 (t0) REVERT: D 718 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8736 (pp) REVERT: E 245 MET cc_start: 0.6091 (mpp) cc_final: 0.5889 (mpp) REVERT: E 311 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8207 (tm) REVERT: E 390 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7490 (mtpp) REVERT: E 629 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6233 (mmp-170) REVERT: E 722 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7091 (pt) REVERT: F 171 ARG cc_start: 0.6526 (mtp85) cc_final: 0.6057 (mtm180) REVERT: F 371 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8229 (mt) REVERT: F 664 LEU cc_start: 0.9188 (tt) cc_final: 0.8894 (tp) outliers start: 112 outliers final: 67 residues processed: 388 average time/residue: 0.1717 time to fit residues: 108.6710 Evaluate side-chains 342 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 264 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 629 ARG Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 87 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN C 201 ASN C 575 GLN E 159 GLN E 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092615 restraints weight = 57827.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094162 restraints weight = 38683.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.096265 restraints weight = 26652.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096531 restraints weight = 21794.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096323 restraints weight = 18199.415| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27694 Z= 0.230 Angle : 0.754 12.656 37477 Z= 0.369 Chirality : 0.047 0.288 4300 Planarity : 0.006 0.118 4894 Dihedral : 10.608 178.168 4101 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.82 % Favored : 89.01 % Rotamer: Outliers : 4.23 % Allowed : 17.78 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -2.22 (0.14), residues: 3484 helix: -0.35 (0.14), residues: 1568 sheet: -2.24 (0.25), residues: 360 loop : -2.47 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 333 TYR 0.020 0.002 TYR E 658 PHE 0.023 0.002 PHE A 605 TRP 0.016 0.002 TRP E 545 HIS 0.007 0.001 HIS E 685 Details of bonding type rmsd covalent geometry : bond 0.00536 (27694) covalent geometry : angle 0.75416 (37477) hydrogen bonds : bond 0.04049 ( 892) hydrogen bonds : angle 4.56051 ( 2526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 267 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: A 769 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9106 (mm) REVERT: B 217 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: B 605 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8591 (p90) REVERT: B 703 ASP cc_start: 0.8687 (p0) cc_final: 0.8348 (p0) REVERT: B 827 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: C 164 TYR cc_start: 0.8064 (m-80) cc_final: 0.7743 (m-10) REVERT: C 604 MET cc_start: 0.8504 (ttp) cc_final: 0.8132 (ptm) REVERT: C 769 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7904 (mm) REVERT: C 822 MET cc_start: 0.8161 (ppp) cc_final: 0.7881 (ppp) REVERT: D 584 ASP cc_start: 0.7835 (m-30) cc_final: 0.7165 (t0) REVERT: D 718 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8850 (pp) REVERT: E 311 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8291 (tm) REVERT: E 390 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7472 (mtpp) REVERT: E 604 MET cc_start: 0.8550 (ppp) cc_final: 0.8260 (ppp) REVERT: F 171 ARG cc_start: 0.6576 (mtp85) cc_final: 0.6030 (mtm180) REVERT: F 371 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8278 (mt) REVERT: F 664 LEU cc_start: 0.9258 (tt) cc_final: 0.8961 (tp) REVERT: F 824 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8853 (pp) outliers start: 118 outliers final: 83 residues processed: 361 average time/residue: 0.1683 time to fit residues: 99.8606 Evaluate side-chains 343 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 250 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 659 GLU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 277 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 192 GLN B 201 ASN E 159 GLN F 705 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094274 restraints weight = 57330.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095799 restraints weight = 37041.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097201 restraints weight = 25365.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097527 restraints weight = 22754.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097442 restraints weight = 19282.074| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27694 Z= 0.134 Angle : 0.689 15.585 37477 Z= 0.334 Chirality : 0.044 0.292 4300 Planarity : 0.005 0.119 4894 Dihedral : 10.261 178.948 4101 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.87 % Favored : 89.95 % Rotamer: Outliers : 4.12 % Allowed : 17.92 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.92 (0.15), residues: 3484 helix: -0.12 (0.14), residues: 1561 sheet: -1.95 (0.27), residues: 340 loop : -2.32 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 629 TYR 0.021 0.001 TYR E 658 PHE 0.022 0.002 PHE A 623 TRP 0.010 0.001 TRP B 545 HIS 0.007 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00308 (27694) covalent geometry : angle 0.68853 (37477) hydrogen bonds : bond 0.03433 ( 892) hydrogen bonds : angle 4.36208 ( 2526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 293 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: A 769 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9070 (mm) REVERT: B 217 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: B 703 ASP cc_start: 0.8643 (p0) cc_final: 0.8348 (p0) REVERT: B 827 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: C 164 TYR cc_start: 0.8009 (m-80) cc_final: 0.7726 (m-10) REVERT: C 442 LEU cc_start: 0.2316 (OUTLIER) cc_final: 0.2035 (mt) REVERT: C 603 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7589 (p90) REVERT: C 604 MET cc_start: 0.8448 (ttp) cc_final: 0.8138 (ptm) REVERT: C 732 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8545 (tp) REVERT: C 769 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7877 (mm) REVERT: C 822 MET cc_start: 0.8166 (ppp) cc_final: 0.7910 (ppp) REVERT: C 827 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: D 584 ASP cc_start: 0.7877 (m-30) cc_final: 0.7215 (t0) REVERT: D 718 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8754 (pp) REVERT: E 311 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8259 (tm) REVERT: E 390 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7511 (mtpt) REVERT: E 604 MET cc_start: 0.8552 (ppp) cc_final: 0.8217 (ppp) REVERT: E 629 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6325 (mmp-170) REVERT: F 171 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6034 (mtm180) REVERT: F 371 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8274 (mt) REVERT: F 664 LEU cc_start: 0.9144 (tt) cc_final: 0.8869 (tp) REVERT: F 824 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8868 (pp) outliers start: 115 outliers final: 81 residues processed: 392 average time/residue: 0.1675 time to fit residues: 108.1022 Evaluate side-chains 353 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 258 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 629 ARG Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 191 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 287 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 827 GLN E 159 GLN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096354 restraints weight = 56995.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097852 restraints weight = 37571.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099610 restraints weight = 24965.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099881 restraints weight = 21064.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099866 restraints weight = 18524.966| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27694 Z= 0.111 Angle : 0.678 13.271 37477 Z= 0.328 Chirality : 0.043 0.284 4300 Planarity : 0.005 0.120 4894 Dihedral : 9.894 177.256 4101 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 3.15 % Allowed : 19.68 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.72 (0.15), residues: 3484 helix: 0.03 (0.14), residues: 1558 sheet: -1.68 (0.27), residues: 344 loop : -2.22 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 629 TYR 0.020 0.001 TYR E 658 PHE 0.018 0.001 PHE C 623 TRP 0.008 0.001 TRP E 545 HIS 0.014 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00243 (27694) covalent geometry : angle 0.67803 (37477) hydrogen bonds : bond 0.03065 ( 892) hydrogen bonds : angle 4.19052 ( 2526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 307 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8649 (p0) cc_final: 0.8342 (p0) REVERT: A 629 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6705 (mtm-85) REVERT: A 680 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: A 769 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 200 ASN cc_start: 0.9247 (p0) cc_final: 0.8928 (p0) REVERT: B 217 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: B 605 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8566 (p90) REVERT: B 703 ASP cc_start: 0.8595 (p0) cc_final: 0.8348 (p0) REVERT: B 827 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: C 164 TYR cc_start: 0.7971 (m-80) cc_final: 0.7762 (m-10) REVERT: C 732 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8550 (tp) REVERT: C 769 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7862 (mm) REVERT: C 822 MET cc_start: 0.8143 (ppp) cc_final: 0.7939 (ppp) REVERT: C 827 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: D 192 GLN cc_start: 0.8379 (pt0) cc_final: 0.7744 (pp30) REVERT: D 584 ASP cc_start: 0.7850 (m-30) cc_final: 0.7227 (t0) REVERT: D 718 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8641 (pp) REVERT: E 245 MET cc_start: 0.6143 (mpp) cc_final: 0.5759 (mpp) REVERT: E 311 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8254 (tm) REVERT: E 390 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7436 (mtpt) REVERT: E 604 MET cc_start: 0.8512 (ppp) cc_final: 0.8200 (ppp) REVERT: F 171 ARG cc_start: 0.6527 (mtp85) cc_final: 0.6049 (mtm180) REVERT: F 371 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8256 (mt) REVERT: F 631 MET cc_start: 0.8684 (ppp) cc_final: 0.8422 (ptt) REVERT: F 664 LEU cc_start: 0.9080 (tt) cc_final: 0.8800 (tp) REVERT: F 756 LEU cc_start: 0.8368 (mt) cc_final: 0.7987 (mp) REVERT: F 824 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (pp) REVERT: F 827 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8238 (pt0) outliers start: 88 outliers final: 61 residues processed: 383 average time/residue: 0.1667 time to fit residues: 105.5562 Evaluate side-chains 351 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 71 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN E 159 GLN F 200 ASN F 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095982 restraints weight = 57112.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097430 restraints weight = 38691.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099218 restraints weight = 26217.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099439 restraints weight = 21596.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099570 restraints weight = 19217.388| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27694 Z= 0.116 Angle : 0.679 15.031 37477 Z= 0.327 Chirality : 0.043 0.278 4300 Planarity : 0.005 0.117 4894 Dihedral : 9.719 171.184 4101 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.24 % Favored : 90.61 % Rotamer: Outliers : 3.44 % Allowed : 19.35 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.57 (0.15), residues: 3484 helix: 0.15 (0.14), residues: 1552 sheet: -1.58 (0.28), residues: 336 loop : -2.15 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 780 TYR 0.013 0.001 TYR F 338 PHE 0.015 0.001 PHE B 386 TRP 0.008 0.001 TRP B 545 HIS 0.011 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00263 (27694) covalent geometry : angle 0.67949 (37477) hydrogen bonds : bond 0.03044 ( 892) hydrogen bonds : angle 4.13456 ( 2526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 287 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8670 (p0) cc_final: 0.8367 (p0) REVERT: A 680 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: A 769 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9021 (mm) REVERT: B 217 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: B 327 ASP cc_start: 0.7444 (t0) cc_final: 0.6561 (m-30) REVERT: B 605 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8521 (p90) REVERT: B 703 ASP cc_start: 0.8586 (p0) cc_final: 0.8329 (p0) REVERT: B 827 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: C 603 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7520 (p90) REVERT: C 732 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 769 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7829 (mm) REVERT: C 822 MET cc_start: 0.8154 (ppp) cc_final: 0.7862 (ppp) REVERT: C 827 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: D 192 GLN cc_start: 0.8380 (pt0) cc_final: 0.7897 (pp30) REVERT: D 584 ASP cc_start: 0.7858 (m-30) cc_final: 0.7221 (t0) REVERT: D 718 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8659 (pp) REVERT: E 245 MET cc_start: 0.6027 (mpp) cc_final: 0.5683 (mpp) REVERT: E 311 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8247 (tm) REVERT: E 390 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7407 (mtpt) REVERT: E 604 MET cc_start: 0.8469 (ppp) cc_final: 0.8189 (ppp) REVERT: F 171 ARG cc_start: 0.6518 (mtp85) cc_final: 0.6045 (mtm180) REVERT: F 371 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8288 (mt) REVERT: F 631 MET cc_start: 0.8712 (ppp) cc_final: 0.8427 (ptt) REVERT: F 664 LEU cc_start: 0.9097 (tt) cc_final: 0.8833 (tp) REVERT: F 756 LEU cc_start: 0.8374 (mt) cc_final: 0.7980 (mp) REVERT: F 827 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8543 (pm20) outliers start: 96 outliers final: 66 residues processed: 368 average time/residue: 0.1702 time to fit residues: 102.5294 Evaluate side-chains 339 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.0050 chunk 232 optimal weight: 4.9990 chunk 208 optimal weight: 0.1980 chunk 216 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 290 optimal weight: 0.0570 chunk 64 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 192 GLN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097648 restraints weight = 57045.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099076 restraints weight = 36510.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100905 restraints weight = 24915.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100949 restraints weight = 21170.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101088 restraints weight = 18572.252| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27694 Z= 0.110 Angle : 0.690 14.850 37477 Z= 0.328 Chirality : 0.043 0.275 4300 Planarity : 0.005 0.115 4894 Dihedral : 9.430 164.336 4101 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 2.65 % Allowed : 20.43 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.48 (0.15), residues: 3484 helix: 0.20 (0.14), residues: 1555 sheet: -1.50 (0.28), residues: 346 loop : -2.08 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 409 TYR 0.023 0.001 TYR E 658 PHE 0.036 0.001 PHE C 623 TRP 0.007 0.001 TRP E 545 HIS 0.011 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00243 (27694) covalent geometry : angle 0.68998 (37477) hydrogen bonds : bond 0.02795 ( 892) hydrogen bonds : angle 4.04677 ( 2526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8625 (p0) cc_final: 0.8386 (p0) REVERT: A 680 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: A 769 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 217 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: B 327 ASP cc_start: 0.7528 (t0) cc_final: 0.6619 (m-30) REVERT: B 703 ASP cc_start: 0.8566 (p0) cc_final: 0.8330 (p0) REVERT: B 827 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: C 732 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8607 (tp) REVERT: C 769 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7846 (mm) REVERT: C 822 MET cc_start: 0.8143 (ppp) cc_final: 0.7865 (ppp) REVERT: C 827 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: D 192 GLN cc_start: 0.8319 (pt0) cc_final: 0.7872 (pp30) REVERT: D 584 ASP cc_start: 0.7808 (m-30) cc_final: 0.7214 (t0) REVERT: D 718 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8626 (pp) REVERT: E 245 MET cc_start: 0.6020 (mpp) cc_final: 0.5656 (mpp) REVERT: E 311 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8209 (tm) REVERT: E 325 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5444 (mt-10) REVERT: E 604 MET cc_start: 0.8439 (ppp) cc_final: 0.8158 (ppp) REVERT: F 171 ARG cc_start: 0.6462 (mtp85) cc_final: 0.6071 (mtm180) REVERT: F 371 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8257 (mt) REVERT: F 664 LEU cc_start: 0.9053 (tt) cc_final: 0.8820 (tp) REVERT: F 756 LEU cc_start: 0.8296 (mt) cc_final: 0.7904 (mp) outliers start: 74 outliers final: 55 residues processed: 360 average time/residue: 0.1633 time to fit residues: 96.7797 Evaluate side-chains 343 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 271 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 259 optimal weight: 0.0770 chunk 152 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 192 GLN C 201 ASN F 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095779 restraints weight = 56984.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097290 restraints weight = 37462.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099015 restraints weight = 25419.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099127 restraints weight = 22307.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099147 restraints weight = 19225.707| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27694 Z= 0.135 Angle : 0.694 14.613 37477 Z= 0.331 Chirality : 0.044 0.272 4300 Planarity : 0.005 0.112 4894 Dihedral : 9.459 157.615 4101 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.13 % Favored : 90.76 % Rotamer: Outliers : 2.87 % Allowed : 20.50 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.42 (0.15), residues: 3484 helix: 0.29 (0.14), residues: 1554 sheet: -1.58 (0.27), residues: 353 loop : -2.07 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 409 TYR 0.021 0.001 TYR E 658 PHE 0.022 0.001 PHE C 623 TRP 0.010 0.001 TRP B 545 HIS 0.011 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00314 (27694) covalent geometry : angle 0.69406 (37477) hydrogen bonds : bond 0.03042 ( 892) hydrogen bonds : angle 4.06777 ( 2526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.13 seconds wall clock time: 76 minutes 0.16 seconds (4560.16 seconds total)