Starting phenix.real_space_refine on Mon Sep 14 04:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.cif" model { file = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_7943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djv_7943/09_2026/6djv_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.78, per 1000 atoms: 0.25 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 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: 0.91 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: 5.11 Time building geometry restraints manager: 3.41 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: 16621 32.67 - 65.33: 290 65.33 - 98.00: 25 98.00 - 130.67: 3 130.67 - 163.34: 3 Dihedral angle restraints: 16942 sinusoidal: 6906 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 16939 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.100 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 12.812 163.336 10478 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/Z covalent geometry : bond 0.00639 / 0.32 (27694) covalent geometry : angle 1.11036 / 0.62 (37477) hydrogen bonds : bond 0.19974 / 13.31 ( 892) hydrogen bonds : angle 7.71337 / 5.39 ( 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 : 1.512 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: 0.7015 (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: 0.7752 (p) cc_final: 0.7401 (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: 0.2410 time to fit residues: 274.2770 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 : 0.969 ------------------------------------------------------------------------------- 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... 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 = 0.3589 r_free = 0.3589 target = 0.121590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096141 restraints weight = 57320.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098030 restraints weight = 36472.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099381 restraints weight = 26858.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100190 restraints weight = 21980.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101100 restraints weight = 19383.351| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27694 Z= 0.149 Angle : 0.742 15.942 37477 Z= 0.374 Chirality : 0.044 0.218 4300 Planarity : 0.006 0.097 4894 Dihedral : 9.899 147.569 4010 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.73 % Favored : 89.09 % Rotamer: Outliers : 2.62 % Allowed : 12.72 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.23 % 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: -3.49 (0.13), residues: 3484 helix: -1.80 (0.12), residues: 1530 sheet: -2.19 (0.28), residues: 316 loop : -2.83 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 352 TYR 0.026 0.002 TYR F 338 PHE 0.021 0.002 PHE D 625 TRP 0.019 0.002 TRP D 792 HIS 0.004 0.001 HIS C 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (27694) covalent geometry : angle 0.74249 / 0.37 (37477) hydrogen bonds : bond 0.04356 / 3.00 ( 892) hydrogen bonds : angle 5.05561 / 3.52 ( 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 486 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 413 time to evaluate : 1.085 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: 0.7369 (mp0) REVERT: B 680 GLU cc_start: 0.7750 (mp0) cc_final: 0.7302 (mm-30) REVERT: B 703 ASP cc_start: 0.8734 (p0) cc_final: 0.8219 (p0) REVERT: C 623 PHE cc_start: 0.7113 (p90) cc_final: 0.6862 (p90) REVERT: C 732 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8728 (tp) REVERT: D 257 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7505 (tp30) REVERT: D 299 MET cc_start: 0.8304 (mpp) cc_final: 0.8072 (mpp) REVERT: D 355 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8629 (ttpp) REVERT: D 564 MET cc_start: 0.7983 (ptm) cc_final: 0.7781 (ptm) REVERT: D 584 ASP cc_start: 0.7780 (m-30) cc_final: 0.7056 (t0) REVERT: D 718 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8666 (pp) REVERT: E 192 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8291 (tm-30) REVERT: E 200 ASN cc_start: 0.8709 (p0) cc_final: 0.8229 (p0) REVERT: E 311 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8089 (tm) REVERT: E 390 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7649 (mtpp) REVERT: F 171 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6434 (mtp180) REVERT: F 244 SER cc_start: 0.7904 (p) cc_final: 0.7650 (t) REVERT: F 692 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8658 (tt) REVERT: F 732 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8912 (tm) outliers start: 73 outliers final: 33 residues processed: 466 average time/residue: 0.1830 time to fit residues: 136.5754 Evaluate side-chains 351 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 355 LYS 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 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: 5.9990 chunk 199 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 597 ASN B 685 HIS ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS F 784 GLN ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092779 restraints weight = 57767.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094888 restraints weight = 37463.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096380 restraints weight = 27661.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097237 restraints weight = 22464.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098074 restraints weight = 19664.204| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27694 Z= 0.188 Angle : 0.736 13.503 37477 Z= 0.366 Chirality : 0.045 0.223 4300 Planarity : 0.006 0.108 4894 Dihedral : 9.558 162.040 3994 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.94 % Favored : 88.89 % Rotamer: Outliers : 4.16 % Allowed : 14.84 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.52 % 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: -2.80 (0.14), residues: 3484 helix: -0.96 (0.13), residues: 1558 sheet: -2.14 (0.27), residues: 324 loop : -2.72 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 791 TYR 0.020 0.002 TYR F 338 PHE 0.027 0.002 PHE D 798 TRP 0.020 0.002 TRP D 792 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (27694) covalent geometry : angle 0.73649 / 0.37 (37477) hydrogen bonds : bond 0.04196 / 2.88 ( 892) hydrogen bonds : angle 4.69562 / 3.27 ( 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 432 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 316 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 636 MET cc_start: 0.7828 (mtt) cc_final: 0.7613 (mtt) REVERT: B 703 ASP cc_start: 0.8665 (p0) cc_final: 0.8333 (p0) REVERT: C 732 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 769 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7998 (mm) REVERT: C 817 ASP cc_start: 0.7040 (p0) cc_final: 0.6773 (p0) REVERT: D 257 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7744 (tp30) REVERT: D 299 MET cc_start: 0.8460 (mpp) cc_final: 0.8207 (mpp) REVERT: D 584 ASP cc_start: 0.7835 (m-30) cc_final: 0.7191 (t0) REVERT: D 718 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8811 (pp) REVERT: E 311 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8246 (tm) REVERT: E 390 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7601 (mtpp) REVERT: F 171 ARG cc_start: 0.6836 (mtp85) cc_final: 0.6343 (mtm180) REVERT: F 371 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8141 (mt) REVERT: F 397 GLU cc_start: 0.8416 (tp30) cc_final: 0.8203 (tp30) REVERT: F 692 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8660 (tt) outliers start: 116 outliers final: 61 residues processed: 409 average time/residue: 0.1728 time to fit residues: 114.1514 Evaluate side-chains 341 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 389 ASP 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 748 ASP Chi-restraints excluded: chain A residue 772 LEU 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 324 ILE Chi-restraints excluded: chain B residue 404 MET 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 B residue 702 THR 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 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 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 315 THR Chi-restraints excluded: chain D residue 369 SER 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 838 VAL 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 629 ARG Chi-restraints excluded: chain E residue 648 LEU 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 371 LEU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 545 TRP 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 692 LEU Chi-restraints excluded: chain F residue 772 LEU 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: 0.0010 chunk 56 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 GLN C 721 ASN D 643 HIS E 685 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 827 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 = 0.3507 r_free = 0.3507 target = 0.116139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091896 restraints weight = 58010.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093750 restraints weight = 38025.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095192 restraints weight = 26554.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095442 restraints weight = 22618.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095494 restraints weight = 19783.083| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 27694 Z= 0.239 Angle : 0.769 12.375 37477 Z= 0.380 Chirality : 0.047 0.230 4300 Planarity : 0.006 0.113 4894 Dihedral : 9.536 174.970 3993 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.71 % Favored : 88.12 % Rotamer: Outliers : 4.19 % Allowed : 16.34 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.82 % 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: -2.56 (0.14), residues: 3484 helix: -0.70 (0.13), residues: 1562 sheet: -2.15 (0.26), residues: 349 loop : -2.62 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 598 TYR 0.022 0.002 TYR E 658 PHE 0.027 0.003 PHE B 605 TRP 0.021 0.002 TRP B 545 HIS 0.008 0.002 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (27694) covalent geometry : angle 0.76864 / 0.38 (37477) hydrogen bonds : bond 0.04262 / 2.91 ( 892) hydrogen bonds : angle 4.69771 / 3.28 ( 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 403 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 286 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7027 (p0) REVERT: B 217 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: B 636 MET cc_start: 0.8075 (mtt) cc_final: 0.7833 (mtt) REVERT: B 703 ASP cc_start: 0.8668 (p0) cc_final: 0.8402 (p0) REVERT: B 827 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 564 MET cc_start: 0.7830 (tpp) cc_final: 0.7391 (tpt) REVERT: C 769 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8058 (mm) REVERT: C 822 MET cc_start: 0.8182 (ppp) cc_final: 0.7734 (ppp) REVERT: D 257 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7709 (tp30) REVERT: D 564 MET cc_start: 0.7988 (ptm) cc_final: 0.7550 (ptp) REVERT: D 584 ASP cc_start: 0.7774 (m-30) cc_final: 0.7004 (t0) REVERT: D 718 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8804 (pp) REVERT: E 181 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8323 (pt) REVERT: E 311 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8305 (tm) REVERT: E 390 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7535 (mtpp) REVERT: F 171 ARG cc_start: 0.6653 (mtp85) cc_final: 0.5994 (mtm180) REVERT: F 371 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8193 (mt) REVERT: F 397 GLU cc_start: 0.8436 (tp30) cc_final: 0.8214 (tp30) REVERT: F 664 LEU cc_start: 0.9296 (tt) cc_final: 0.8976 (tp) REVERT: F 692 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8542 (tt) REVERT: F 824 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8863 (pp) outliers start: 117 outliers final: 76 residues processed: 383 average time/residue: 0.1714 time to fit residues: 108.1404 Evaluate side-chains 338 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 319 GLU 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 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 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 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 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 383 THR Chi-restraints excluded: chain D residue 572 VAL 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 207 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 240 LEU 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 629 ARG Chi-restraints excluded: chain E residue 648 LEU 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 371 LEU Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 586 VAL 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 692 LEU 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: 5.9990 chunk 311 optimal weight: 0.0270 chunk 307 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 GLN B 361 HIS C 201 ASN C 575 GLN F 663 GLN F 705 HIS ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094072 restraints weight = 57485.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095860 restraints weight = 37327.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097724 restraints weight = 25829.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097863 restraints weight = 21837.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097983 restraints weight = 18751.133| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27694 Z= 0.139 Angle : 0.684 16.001 37477 Z= 0.333 Chirality : 0.044 0.246 4300 Planarity : 0.005 0.096 4894 Dihedral : 9.084 177.557 3993 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.16 % Favored : 89.67 % Rotamer: Outliers : 4.27 % Allowed : 16.95 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -2.15 (0.14), residues: 3484 helix: -0.33 (0.14), residues: 1540 sheet: -1.89 (0.28), residues: 314 loop : -2.45 (0.15), residues: 1630 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 0.017 0.002 PHE B 386 TRP 0.019 0.002 TRP E 545 HIS 0.005 0.001 HIS E 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27694) covalent geometry : angle 0.68413 / 0.33 (37477) hydrogen bonds : bond 0.03490 / 2.39 ( 892) hydrogen bonds : angle 4.42735 / 3.11 ( 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 418 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 299 time to evaluate : 1.095 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: 0.8316 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 605 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8639 (p90) REVERT: B 636 MET cc_start: 0.8152 (mtt) cc_final: 0.7945 (mtt) REVERT: B 703 ASP cc_start: 0.8606 (p0) cc_final: 0.8324 (p0) REVERT: B 827 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: C 604 MET cc_start: 0.8412 (ttp) cc_final: 0.8165 (ptm) REVERT: C 732 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 769 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7993 (mm) REVERT: C 817 ASP cc_start: 0.7100 (p0) cc_final: 0.6810 (p0) REVERT: C 822 MET cc_start: 0.8101 (ppp) cc_final: 0.7847 (ppp) REVERT: D 257 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7759 (tp30) REVERT: D 355 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8584 (ttpp) REVERT: D 584 ASP cc_start: 0.7813 (m-30) cc_final: 0.7127 (t0) REVERT: D 718 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8696 (pp) REVERT: E 311 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8246 (tm) REVERT: E 629 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6323 (mmp-170) REVERT: F 171 ARG cc_start: 0.6581 (mtp85) cc_final: 0.5927 (mtm180) REVERT: F 371 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8235 (mt) REVERT: F 664 LEU cc_start: 0.9251 (tt) cc_final: 0.8961 (tp) REVERT: F 692 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8642 (tt) REVERT: F 824 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8811 (pp) outliers start: 119 outliers final: 68 residues processed: 401 average time/residue: 0.1667 time to fit residues: 108.9682 Evaluate side-chains 351 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 271 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 692 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 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 343 SER Chi-restraints excluded: chain B residue 346 ASP 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 645 VAL 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 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 834 VAL 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 355 LYS Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 641 GLU 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 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 629 ARG 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 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 692 LEU Chi-restraints excluded: chain F residue 722 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 87 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 316 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 GLN C 201 ASN D 362 HIS E 159 GLN ** 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 = 0.3479 r_free = 0.3479 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.089947 restraints weight = 58308.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091576 restraints weight = 38678.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093728 restraints weight = 26790.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093847 restraints weight = 20394.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093844 restraints weight = 19108.746| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4375 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= 0.299 Angle : 0.817 12.883 37477 Z= 0.405 Chirality : 0.049 0.295 4300 Planarity : 0.006 0.122 4894 Dihedral : 9.195 177.123 3991 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.91 % Favored : 87.89 % Rotamer: Outliers : 5.20 % Allowed : 17.35 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.82 % 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: -2.31 (0.14), residues: 3484 helix: -0.40 (0.13), residues: 1552 sheet: -2.31 (0.25), residues: 367 loop : -2.51 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 333 TYR 0.022 0.002 TYR E 658 PHE 0.028 0.003 PHE A 605 TRP 0.022 0.002 TRP C 545 HIS 0.008 0.002 HIS E 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.30 (27694) covalent geometry : angle 0.81687 / 0.40 (37477) hydrogen bonds : bond 0.04595 / 3.13 ( 892) hydrogen bonds : angle 4.76430 / 3.32 ( 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 401 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 256 time to evaluate : 1.088 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: B 217 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: B 605 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8630 (p90) REVERT: B 703 ASP cc_start: 0.8718 (p0) cc_final: 0.8370 (p0) REVERT: C 442 LEU cc_start: 0.2410 (OUTLIER) cc_final: 0.2135 (mt) REVERT: C 553 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7878 (pp) REVERT: C 603 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7863 (p90) REVERT: C 604 MET cc_start: 0.8499 (ttp) cc_final: 0.8140 (ptm) REVERT: C 769 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7842 (mm) REVERT: C 822 MET cc_start: 0.8182 (ppp) cc_final: 0.7886 (ppp) REVERT: C 827 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7036 (pt0) REVERT: D 257 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7818 (tp30) REVERT: D 355 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8595 (ttpp) REVERT: D 387 LEU cc_start: 0.9102 (tp) cc_final: 0.8888 (tt) REVERT: D 584 ASP cc_start: 0.7899 (m-30) cc_final: 0.7168 (t0) REVERT: D 605 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8032 (p90) REVERT: D 718 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8808 (pp) REVERT: E 311 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8359 (tm) REVERT: E 604 MET cc_start: 0.8595 (ppp) cc_final: 0.8297 (ppp) REVERT: E 802 TYR cc_start: 0.7076 (m-80) cc_final: 0.6874 (m-80) REVERT: F 171 ARG cc_start: 0.6621 (mtp85) cc_final: 0.5963 (mtm180) REVERT: F 371 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8301 (mt) REVERT: F 664 LEU cc_start: 0.9298 (tt) cc_final: 0.8999 (tp) REVERT: F 692 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8600 (tt) REVERT: F 824 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8829 (pp) outliers start: 145 outliers final: 95 residues processed: 382 average time/residue: 0.1627 time to fit residues: 102.7827 Evaluate side-chains 349 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 240 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 300 ILE 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 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 693 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 163 LYS 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 324 ILE Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 416 VAL 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 609 THR 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 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 283 ILE 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 442 LEU Chi-restraints excluded: chain C residue 553 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 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 165 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 641 GLU 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 808 ARG Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 240 LEU 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 605 PHE Chi-restraints excluded: chain E residue 627 ASP 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 837 ASN Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 586 VAL Chi-restraints excluded: chain F residue 615 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 692 LEU Chi-restraints excluded: chain F residue 709 VAL 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: 3.9990 chunk 268 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 0.0570 chunk 237 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 293 optimal weight: 10.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN B 201 ASN D 827 GLN 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 = 0.3555 r_free = 0.3555 target = 0.119146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095612 restraints weight = 57033.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097131 restraints weight = 37055.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098643 restraints weight = 25093.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098881 restraints weight = 22400.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098899 restraints weight = 19019.433| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27694 Z= 0.112 Angle : 0.676 12.905 37477 Z= 0.329 Chirality : 0.043 0.287 4300 Planarity : 0.005 0.109 4894 Dihedral : 8.572 170.864 3991 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.81 % Favored : 91.04 % Rotamer: Outliers : 3.48 % Allowed : 18.82 % Favored : 77.71 % 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: -1.81 (0.15), residues: 3484 helix: -0.00 (0.14), residues: 1544 sheet: -1.88 (0.28), residues: 315 loop : -2.28 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 629 TYR 0.026 0.001 TYR E 658 PHE 0.020 0.002 PHE B 386 TRP 0.010 0.001 TRP E 545 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27694) covalent geometry : angle 0.67616 / 0.33 (37477) hydrogen bonds : bond 0.03121 / 2.13 ( 892) hydrogen bonds : angle 4.28293 / 3.01 ( 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 400 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 303 time to evaluate : 1.040 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: B 217 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: B 703 ASP cc_start: 0.8644 (p0) cc_final: 0.8343 (p0) REVERT: B 827 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: C 732 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 769 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 822 MET cc_start: 0.8107 (ppp) cc_final: 0.7899 (ppp) REVERT: C 827 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: D 192 GLN cc_start: 0.8408 (pt0) cc_final: 0.7672 (pp30) REVERT: D 355 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8392 (ttpp) REVERT: D 584 ASP cc_start: 0.7837 (m-30) cc_final: 0.7205 (t0) REVERT: E 311 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8248 (tm) REVERT: E 604 MET cc_start: 0.8480 (ppp) cc_final: 0.8162 (ppp) REVERT: E 693 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (mt) REVERT: F 171 ARG cc_start: 0.6651 (mtp85) cc_final: 0.6056 (mtm180) REVERT: F 311 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (tm) REVERT: F 371 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8284 (mt) REVERT: F 664 LEU cc_start: 0.9165 (tt) cc_final: 0.8896 (tp) REVERT: F 692 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 97 outliers final: 57 residues processed: 389 average time/residue: 0.1571 time to fit residues: 102.5844 Evaluate side-chains 337 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 246 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 635 ASP 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 702 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 ILE 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 350 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 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 193 VAL 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 355 LYS Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 675 VAL 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 693 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN 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 237 ILE Chi-restraints excluded: chain F residue 311 LEU 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 692 LEU Chi-restraints excluded: chain F residue 772 LEU 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: 4.9990 chunk 26 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 104 optimal weight: 0.0370 chunk 287 optimal weight: 0.0170 chunk 4 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 GLN B 201 ASN F 705 HIS F 771 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095877 restraints weight = 57132.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097666 restraints weight = 37205.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098596 restraints weight = 26757.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099281 restraints weight = 22414.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099583 restraints weight = 19594.845| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27694 Z= 0.109 Angle : 0.683 21.032 37477 Z= 0.328 Chirality : 0.043 0.292 4300 Planarity : 0.005 0.113 4894 Dihedral : 8.260 162.396 3991 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.04 % Favored : 90.82 % Rotamer: Outliers : 2.83 % Allowed : 20.29 % Favored : 76.88 % 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: -1.64 (0.15), residues: 3484 helix: 0.11 (0.14), residues: 1553 sheet: -1.72 (0.29), residues: 320 loop : -2.19 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 780 TYR 0.021 0.001 TYR E 658 PHE 0.017 0.001 PHE B 386 TRP 0.006 0.001 TRP B 545 HIS 0.014 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (27694) covalent geometry : angle 0.68328 / 0.33 (37477) hydrogen bonds : bond 0.02928 / 2.00 ( 892) hydrogen bonds : angle 4.12986 / 2.91 ( 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 386 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 307 time to evaluate : 1.041 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 279 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6821 (mm-30) REVERT: A 597 ASN cc_start: 0.8664 (p0) cc_final: 0.8353 (p0) REVERT: A 629 ARG cc_start: 0.7080 (mtm-85) cc_final: 0.6664 (mtm-85) REVERT: B 217 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: B 703 ASP cc_start: 0.8599 (p0) cc_final: 0.8322 (p0) REVERT: B 827 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: C 618 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8648 (ttmm) REVERT: C 732 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8563 (tp) REVERT: C 769 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7865 (mm) REVERT: C 827 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: D 192 GLN cc_start: 0.8326 (pt0) cc_final: 0.7820 (pp30) REVERT: D 584 ASP cc_start: 0.7854 (m-30) cc_final: 0.7237 (t0) REVERT: D 718 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8596 (pp) REVERT: E 311 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8251 (tm) REVERT: E 604 MET cc_start: 0.8508 (ppp) cc_final: 0.8236 (ppp) REVERT: F 171 ARG cc_start: 0.6638 (mtp85) cc_final: 0.6015 (mtm180) REVERT: F 311 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7948 (tm) REVERT: F 371 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8286 (mt) REVERT: F 664 LEU cc_start: 0.9141 (tt) cc_final: 0.8887 (tp) REVERT: F 692 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (tt) REVERT: F 824 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8809 (pp) outliers start: 79 outliers final: 50 residues processed: 377 average time/residue: 0.1663 time to fit residues: 103.8536 Evaluate side-chains 329 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 300 ILE 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 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP 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 609 THR Chi-restraints excluded: chain B residue 644 THR 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 605 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 620 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 241 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 675 VAL Chi-restraints excluded: chain D residue 718 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 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 237 ILE Chi-restraints excluded: chain F residue 311 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 692 LEU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 824 LEU 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: 7.9990 chunk 120 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 30 optimal weight: 0.0570 chunk 317 optimal weight: 6.9990 chunk 328 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 192 GLN F 200 ASN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096927 restraints weight = 56805.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098541 restraints weight = 36283.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099374 restraints weight = 26584.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100434 restraints weight = 22034.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100451 restraints weight = 18996.676| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27694 Z= 0.110 Angle : 0.679 14.553 37477 Z= 0.325 Chirality : 0.043 0.272 4300 Planarity : 0.005 0.121 4894 Dihedral : 8.008 151.270 3991 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 2.58 % Allowed : 20.61 % Favored : 76.81 % 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: -1.51 (0.15), residues: 3484 helix: 0.22 (0.14), residues: 1548 sheet: -1.62 (0.28), residues: 337 loop : -2.12 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 746 TYR 0.021 0.001 TYR E 658 PHE 0.016 0.001 PHE B 386 TRP 0.007 0.001 TRP B 545 HIS 0.012 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (27694) covalent geometry : angle 0.67942 / 0.32 (37477) hydrogen bonds : bond 0.02826 / 1.92 ( 892) hydrogen bonds : angle 4.03837 / 2.84 ( 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 372 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 300 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 ILE cc_start: 0.9411 (tp) cc_final: 0.9201 (tp) REVERT: B 217 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 703 ASP cc_start: 0.8596 (p0) cc_final: 0.8327 (p0) REVERT: B 827 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: C 618 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8611 (ttmm) REVERT: C 622 ASP cc_start: 0.8312 (m-30) cc_final: 0.8017 (m-30) REVERT: C 732 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 769 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 192 GLN cc_start: 0.8304 (pt0) cc_final: 0.7865 (pp30) REVERT: D 584 ASP cc_start: 0.7812 (m-30) cc_final: 0.7258 (t0) REVERT: D 718 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8461 (pp) REVERT: E 311 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8243 (tm) REVERT: E 325 GLU cc_start: 0.6491 (mm-30) cc_final: 0.5262 (mt-10) REVERT: E 604 MET cc_start: 0.8513 (ppp) cc_final: 0.8187 (ppp) REVERT: E 673 TYR cc_start: 0.8386 (m-10) cc_final: 0.8145 (m-10) REVERT: F 171 ARG cc_start: 0.6565 (mtp85) cc_final: 0.6000 (mtm180) REVERT: F 311 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7927 (tm) REVERT: F 371 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8265 (mt) REVERT: F 664 LEU cc_start: 0.9123 (tt) cc_final: 0.8872 (tp) REVERT: F 756 LEU cc_start: 0.8289 (mt) cc_final: 0.8001 (mp) REVERT: F 822 MET cc_start: 0.7695 (ttm) cc_final: 0.7353 (mtm) outliers start: 72 outliers final: 50 residues processed: 361 average time/residue: 0.1686 time to fit residues: 100.0586 Evaluate side-chains 325 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 300 ILE 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 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP 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 609 THR Chi-restraints excluded: chain B residue 644 THR 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 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 241 ASP Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 675 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 207 GLU Chi-restraints excluded: chain E residue 240 LEU 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 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 237 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.1980 chunk 232 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 290 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095028 restraints weight = 56936.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097171 restraints weight = 36485.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098719 restraints weight = 26797.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099800 restraints weight = 21696.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100484 restraints weight = 18744.841| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27694 Z= 0.114 Angle : 0.688 15.013 37477 Z= 0.327 Chirality : 0.043 0.272 4300 Planarity : 0.005 0.113 4894 Dihedral : 7.878 141.134 3991 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.96 % Favored : 90.96 % Rotamer: Outliers : 2.26 % Allowed : 21.22 % Favored : 76.52 % 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: -1.40 (0.15), residues: 3484 helix: 0.30 (0.14), residues: 1548 sheet: -1.57 (0.28), residues: 346 loop : -2.05 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 780 TYR 0.022 0.001 TYR E 658 PHE 0.034 0.001 PHE C 623 TRP 0.007 0.001 TRP B 545 HIS 0.011 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27694) covalent geometry : angle 0.68799 / 0.33 (37477) hydrogen bonds : bond 0.02843 / 1.95 ( 892) hydrogen bonds : angle 4.00090 / 2.82 ( 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 346 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 283 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: A 681 ILE cc_start: 0.9433 (tp) cc_final: 0.9224 (tp) REVERT: B 217 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 703 ASP cc_start: 0.8601 (p0) cc_final: 0.8316 (p0) REVERT: B 827 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: C 618 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8598 (ttmm) REVERT: C 732 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 769 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 192 GLN cc_start: 0.8345 (pt0) cc_final: 0.7888 (pp30) REVERT: D 584 ASP cc_start: 0.7850 (m-30) cc_final: 0.7296 (t0) REVERT: D 680 GLU cc_start: 0.8166 (pm20) cc_final: 0.7914 (pm20) REVERT: D 718 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8616 (pp) REVERT: E 311 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8249 (tm) REVERT: E 325 GLU cc_start: 0.6330 (mm-30) cc_final: 0.5494 (mt-10) REVERT: E 604 MET cc_start: 0.8522 (ppp) cc_final: 0.8214 (ppp) REVERT: E 673 TYR cc_start: 0.8417 (m-10) cc_final: 0.8175 (m-10) REVERT: E 819 LEU cc_start: 0.9325 (pp) cc_final: 0.9125 (pp) REVERT: F 171 ARG cc_start: 0.6548 (mtp85) cc_final: 0.6087 (mtm180) REVERT: F 371 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8237 (mt) REVERT: F 664 LEU cc_start: 0.9136 (tt) cc_final: 0.8881 (tp) REVERT: F 756 LEU cc_start: 0.8263 (mt) cc_final: 0.7963 (mp) REVERT: F 822 MET cc_start: 0.7641 (ttm) cc_final: 0.7374 (mtm) outliers start: 63 outliers final: 50 residues processed: 335 average time/residue: 0.1692 time to fit residues: 93.5976 Evaluate side-chains 326 residues out of total 2852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 300 ILE 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 664 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP 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 609 THR Chi-restraints excluded: chain B residue 644 THR 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 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 834 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 675 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 207 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 299 MET 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 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 237 ILE 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 553 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 238 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 324 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093902 restraints weight = 56877.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095915 restraints weight = 36768.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097472 restraints weight = 27155.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098560 restraints weight = 22007.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099244 restraints weight = 19049.600| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4932 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= 0.132 Angle : 0.701 14.012 37477 Z= 0.334 Chirality : 0.044 0.271 4300 Planarity : 0.005 0.119 4894 Dihedral : 7.858 132.871 3991 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.30 % Favored : 90.61 % Rotamer: Outliers : 2.54 % Allowed : 21.25 % Favored : 76.20 % 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: -1.36 (0.15), residues: 3484 helix: 0.34 (0.14), residues: 1547 sheet: -1.65 (0.27), residues: 354 loop : -2.00 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 780 TYR 0.022 0.001 TYR E 658 PHE 0.021 0.001 PHE C 623 TRP 0.010 0.001 TRP B 545 HIS 0.013 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (27694) covalent geometry : angle 0.70089 / 0.33 (37477) hydrogen bonds : bond 0.02998 / 2.04 ( 892) hydrogen bonds : angle 4.02726 / 2.84 ( 2526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4588.20 seconds wall clock time: 79 minutes 47.70 seconds (4787.70 seconds total)