Starting phenix.real_space_refine on Wed Nov 19 21:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.map" model { file = "/net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vhy_8687/11_2025/5vhy_8687.cif" } resolution = 4.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 144 5.16 5 C 17704 2.51 5 N 4558 2.21 5 O 5150 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27572 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6159 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6137 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6159 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6137 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 174} Chain breaks: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.48, per 1000 atoms: 0.24 Number of scatterers: 27572 At special positions: 0 Unit cell: (121.68, 165.36, 197.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4 15.00 F 12 9.00 O 5150 8.00 N 4558 7.00 C 17704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 109 " distance=2.03 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: 2.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6408 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 40 sheets defined 51.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.714A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.675A pdb=" N LYS A 172 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.658A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.637A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.587A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.642A pdb=" N ARG A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.799A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.526A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.792A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 585 removed outlier: 3.820A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 630 removed outlier: 4.125A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.995A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.667A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.781A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.556A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 775 through 782 removed outlier: 3.868A pdb=" N SER A 778 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 782 " --> pdb=" O GLY A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 820 removed outlier: 4.269A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 78 through 93 removed outlier: 4.681A pdb=" N ASN B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.017A pdb=" N ARG B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.502A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.569A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.919A pdb=" N LYS B 234 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.700A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.564A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.638A pdb=" N VAL B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.529A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.577A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.708A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 4.050A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.541A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.820A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.674A pdb=" N ARG B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 774 through 781 Processing helix chain 'B' and resid 789 through 817 removed outlier: 4.126A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.752A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.833A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.764A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.002A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.626A pdb=" N LYS C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.673A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.802A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 514 through 519 removed outlier: 3.835A pdb=" N LEU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.565A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 585 removed outlier: 3.661A pdb=" N MET C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 630 removed outlier: 3.531A pdb=" N VAL C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 4.063A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.639A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 775 through 782 removed outlier: 3.855A pdb=" N SER C 778 " --> pdb=" O ALA C 775 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 782 " --> pdb=" O GLY C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 820 removed outlier: 3.724A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.900A pdb=" N ARG D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.674A pdb=" N LYS D 173 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.658A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.741A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.562A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.580A pdb=" N VAL D 327 " --> pdb=" O TRP D 323 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.748A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.659A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.574A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 585 Processing helix chain 'D' and resid 597 through 626 removed outlier: 4.096A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.064A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.652A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.633A pdb=" N ARG D 715 " --> pdb=" O TYR D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 768 through 771 Processing helix chain 'D' and resid 774 through 781 Processing helix chain 'D' and resid 789 through 817 removed outlier: 4.166A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 118 through 152 Processing helix chain 'E' and resid 158 through 193 removed outlier: 3.704A pdb=" N PHE E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET E 181 " --> pdb=" O MET E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 231 removed outlier: 3.690A pdb=" N LEU E 211 " --> pdb=" O TRP E 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 27 Processing helix chain 'F' and resid 118 through 152 Processing helix chain 'F' and resid 158 through 193 removed outlier: 3.668A pdb=" N PHE F 164 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 231 removed outlier: 4.456A pdb=" N CYS F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 211 " --> pdb=" O TRP F 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.758A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.627A pdb=" N PHE A 133 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS A 132 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 192 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 221 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A 358 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR A 373 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 360 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.454A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.004A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.196A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 17 removed outlier: 6.185A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 73 through 74 removed outlier: 7.105A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.805A pdb=" N ALA B 134 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 192 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.538A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 441 through 444 removed outlier: 6.012A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.810A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 732 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.548A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 17 Processing sheet with id=AC3, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.817A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.296A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 192 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE C 358 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR C 373 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 371 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.705A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.361A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AC9, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.023A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.167A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.094A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 73 through 74 removed outlier: 7.072A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 161 through 164 removed outlier: 6.774A pdb=" N ALA D 134 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 192 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 243 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD6, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AD7, first strand: chain 'D' and resid 441 through 444 removed outlier: 6.027A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.749A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.564A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AE4, first strand: chain 'F' and resid 32 through 33 1381 hydrogen bonds defined for protein. 3987 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: 5.42 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8704 1.35 - 1.48: 7235 1.48 - 1.60: 11981 1.60 - 1.73: 8 1.73 - 1.86: 234 Bond restraints: 28162 Sorted by residual: bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" CAT ZK1 C1101 " pdb=" OAA ZK1 C1101 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" CAT ZK1 D1101 " pdb=" OAA ZK1 D1101 " ideal model delta sigma weight residual 1.214 1.405 -0.191 2.00e-02 2.50e+03 9.14e+01 bond pdb=" CAU ZK1 D1101 " pdb=" OAB ZK1 D1101 " ideal model delta sigma weight residual 1.215 1.402 -0.187 2.00e-02 2.50e+03 8.78e+01 ... (remaining 28157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 34496 1.82 - 3.64: 3150 3.64 - 5.45: 361 5.45 - 7.27: 69 7.27 - 9.09: 12 Bond angle restraints: 38088 Sorted by residual: angle pdb=" C THR B 98 " pdb=" N PRO B 99 " pdb=" CA PRO B 99 " ideal model delta sigma weight residual 119.28 128.37 -9.09 1.10e+00 8.26e-01 6.83e+01 angle pdb=" C THR D 98 " pdb=" N PRO D 99 " pdb=" CA PRO D 99 " ideal model delta sigma weight residual 119.28 128.26 -8.98 1.10e+00 8.26e-01 6.66e+01 angle pdb=" C LYS C 511 " pdb=" N PRO C 512 " pdb=" CA PRO C 512 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C HIS A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.78 125.63 -5.85 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C HIS C 107 " pdb=" N PRO C 108 " pdb=" CA PRO C 108 " ideal model delta sigma weight residual 119.78 125.35 -5.57 1.03e+00 9.43e-01 2.92e+01 ... (remaining 38083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 16338 16.27 - 32.54: 301 32.54 - 48.82: 96 48.82 - 65.09: 14 65.09 - 81.36: 15 Dihedral angle restraints: 16764 sinusoidal: 6740 harmonic: 10024 Sorted by residual: dihedral pdb=" CA SER A 139 " pdb=" C SER A 139 " pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 137 " pdb=" C TYR A 137 " pdb=" N ASP A 138 " pdb=" CA ASP A 138 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN A 318 " pdb=" C ASN A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta harmonic sigma weight residual 0.00 -17.75 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 16761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2509 0.031 - 0.062: 1103 0.062 - 0.094: 468 0.094 - 0.125: 143 0.125 - 0.156: 13 Chirality restraints: 4236 Sorted by residual: chirality pdb=" CA ASP A 519 " pdb=" N ASP A 519 " pdb=" C ASP A 519 " pdb=" CB ASP A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE E 113 " pdb=" N ILE E 113 " pdb=" C ILE E 113 " pdb=" CB ILE E 113 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE F 113 " pdb=" N ILE F 113 " pdb=" C ILE F 113 " pdb=" CB ILE F 113 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 4233 not shown) Planarity restraints: 4768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO C 99 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.060 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO A 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 116 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO E 117 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 117 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 117 " 0.046 5.00e-02 4.00e+02 ... (remaining 4765 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 192 2.44 - 3.06: 20374 3.06 - 3.67: 42605 3.67 - 4.29: 64476 4.29 - 4.90: 98403 Nonbonded interactions: 226050 Sorted by model distance: nonbonded pdb=" O TRP E 31 " pdb=" O GLY E 206 " model vdw 1.831 3.040 nonbonded pdb=" CE2 PHE A 541 " pdb=" CB LEU E 227 " model vdw 1.870 3.740 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.057 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.076 3.040 nonbonded pdb=" CE2 PHE E 187 " pdb=" NE1 TRP E 203 " model vdw 2.103 3.420 ... (remaining 226045 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 817 or resid 1101 through 1102)) selection = chain 'B' selection = (chain 'C' and (resid 10 through 817 or resid 1101 through 1102)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.110 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 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 : 0.007 0.193 28172 Z= 0.453 Angle : 1.267 54.912 38108 Z= 0.831 Chirality : 0.042 0.156 4236 Planarity : 0.005 0.094 4768 Dihedral : 8.406 81.359 10326 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 1.77 % Allowed : 5.24 % Favored : 92.99 % Rotamer: Outliers : 0.17 % Allowed : 0.57 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3452 helix: -1.99 (0.08), residues: 1649 sheet: -2.56 (0.26), residues: 368 loop : 0.49 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 353 TYR 0.019 0.002 TYR B 450 PHE 0.019 0.002 PHE A 574 TRP 0.022 0.002 TRP F 198 HIS 0.006 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00743 (28162) covalent geometry : angle 1.11992 (38088) SS BOND : bond 0.00201 ( 10) SS BOND : angle 25.89950 ( 20) hydrogen bonds : bond 0.17392 ( 1381) hydrogen bonds : angle 8.64972 ( 3987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 623 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 THR cc_start: 0.8435 (m) cc_final: 0.8217 (p) REVERT: A 365 THR cc_start: 0.9049 (m) cc_final: 0.8814 (p) REVERT: A 408 MET cc_start: 0.7709 (mmm) cc_final: 0.7423 (mmm) REVERT: A 440 TYR cc_start: 0.8721 (p90) cc_final: 0.8246 (p90) REVERT: A 442 LEU cc_start: 0.8635 (mt) cc_final: 0.8227 (mt) REVERT: A 496 MET cc_start: 0.7546 (ttm) cc_final: 0.7311 (mtp) REVERT: A 521 LEU cc_start: 0.9067 (tt) cc_final: 0.8549 (tp) REVERT: A 624 LEU cc_start: 0.9110 (mt) cc_final: 0.8460 (tp) REVERT: A 659 PHE cc_start: 0.9137 (m-80) cc_final: 0.8909 (m-80) REVERT: A 674 MET cc_start: 0.8838 (mtm) cc_final: 0.8559 (mtm) REVERT: A 734 ILE cc_start: 0.8617 (mm) cc_final: 0.8280 (mm) REVERT: B 193 ILE cc_start: 0.8837 (mt) cc_final: 0.8009 (mm) REVERT: B 221 ILE cc_start: 0.8582 (mt) cc_final: 0.8029 (mt) REVERT: B 245 PHE cc_start: 0.7833 (m-80) cc_final: 0.7492 (m-10) REVERT: B 403 SER cc_start: 0.8508 (m) cc_final: 0.8306 (p) REVERT: B 412 HIS cc_start: 0.8427 (p90) cc_final: 0.8003 (p90) REVERT: B 463 MET cc_start: 0.8124 (mtm) cc_final: 0.7785 (mtt) REVERT: B 521 LEU cc_start: 0.9352 (tt) cc_final: 0.8660 (tp) REVERT: B 526 TRP cc_start: 0.9099 (m100) cc_final: 0.8550 (m100) REVERT: B 670 MET cc_start: 0.8779 (mtp) cc_final: 0.8433 (mmt) REVERT: C 638 ASP cc_start: 0.9120 (m-30) cc_final: 0.8799 (m-30) REVERT: C 659 PHE cc_start: 0.9392 (m-80) cc_final: 0.8834 (m-80) REVERT: C 674 MET cc_start: 0.9076 (mtm) cc_final: 0.8563 (mtm) REVERT: C 734 ILE cc_start: 0.8650 (mm) cc_final: 0.8336 (mm) REVERT: D 89 CYS cc_start: 0.6879 (m) cc_final: 0.6601 (m) REVERT: D 193 ILE cc_start: 0.8797 (mt) cc_final: 0.8442 (mp) REVERT: D 201 VAL cc_start: 0.9275 (t) cc_final: 0.9016 (t) REVERT: D 221 ILE cc_start: 0.8700 (mt) cc_final: 0.8349 (mm) REVERT: D 245 PHE cc_start: 0.7675 (m-80) cc_final: 0.7439 (m-80) REVERT: D 361 MET cc_start: 0.6236 (mmm) cc_final: 0.5494 (tpp) REVERT: D 403 SER cc_start: 0.8569 (m) cc_final: 0.8332 (p) REVERT: D 463 MET cc_start: 0.7706 (mtm) cc_final: 0.7457 (mtt) REVERT: D 521 LEU cc_start: 0.9267 (tt) cc_final: 0.8722 (tp) REVERT: D 526 TRP cc_start: 0.9174 (m100) cc_final: 0.8674 (m100) REVERT: D 670 MET cc_start: 0.8792 (mtp) cc_final: 0.8221 (mmt) REVERT: E 146 CYS cc_start: 0.5438 (m) cc_final: 0.5122 (t) REVERT: F 146 CYS cc_start: 0.5462 (m) cc_final: 0.5157 (t) outliers start: 5 outliers final: 1 residues processed: 627 average time/residue: 0.1946 time to fit residues: 190.8555 Evaluate side-chains 314 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 46 HIS A 65 GLN A 129 GLN A 214 HIS A 246 GLN A 311 ASN A 337 GLN A 392 GLN A 587 GLN A 619 ASN A 791 ASN B 24 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 355 ASN B 359 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 24 GLN C 83 ASN C 207 GLN C 311 ASN C 325 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 435 HIS D 508 GLN D 587 GLN D 619 ASN D 642 GLN D 714 GLN E 36 GLN E 188 GLN E 228 ASN F 36 GLN F 188 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036695 restraints weight = 203759.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.037957 restraints weight = 124653.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038816 restraints weight = 88135.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039436 restraints weight = 68818.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.039845 restraints weight = 57185.765| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28172 Z= 0.149 Angle : 0.629 9.785 38108 Z= 0.335 Chirality : 0.041 0.231 4236 Planarity : 0.005 0.078 4768 Dihedral : 5.713 74.758 3934 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.06 % Favored : 95.34 % Rotamer: Outliers : 0.10 % Allowed : 1.28 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3452 helix: 0.40 (0.11), residues: 1674 sheet: -2.07 (0.25), residues: 386 loop : 0.13 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 331 TYR 0.025 0.002 TYR B 450 PHE 0.034 0.002 PHE A 541 TRP 0.019 0.002 TRP C 766 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00322 (28162) covalent geometry : angle 0.62389 (38088) SS BOND : bond 0.00504 ( 10) SS BOND : angle 3.67385 ( 20) hydrogen bonds : bond 0.04313 ( 1381) hydrogen bonds : angle 5.64470 ( 3987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 420 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8918 (mm) cc_final: 0.8606 (tp) REVERT: A 129 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8805 (pp30) REVERT: A 161 THR cc_start: 0.8563 (m) cc_final: 0.8206 (p) REVERT: A 260 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8511 (tm-30) REVERT: A 365 THR cc_start: 0.9246 (m) cc_final: 0.9041 (p) REVERT: A 408 MET cc_start: 0.7846 (mmm) cc_final: 0.7359 (mmm) REVERT: A 427 ASP cc_start: 0.8851 (m-30) cc_final: 0.8642 (m-30) REVERT: A 463 MET cc_start: 0.8735 (mtp) cc_final: 0.8400 (mmm) REVERT: A 511 LYS cc_start: 0.8815 (mttt) cc_final: 0.8450 (mmmt) REVERT: A 527 MET cc_start: 0.9428 (mtm) cc_final: 0.9224 (mtt) REVERT: A 624 LEU cc_start: 0.9274 (mt) cc_final: 0.9015 (tp) REVERT: A 670 MET cc_start: 0.8300 (mmm) cc_final: 0.7960 (mmm) REVERT: A 807 MET cc_start: 0.9383 (mmp) cc_final: 0.8852 (mtt) REVERT: B 126 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8688 (mt-10) REVERT: B 221 ILE cc_start: 0.9041 (mt) cc_final: 0.8794 (mm) REVERT: B 361 MET cc_start: 0.6848 (mmm) cc_final: 0.6313 (tpp) REVERT: B 521 LEU cc_start: 0.9199 (tt) cc_final: 0.8333 (tp) REVERT: B 526 TRP cc_start: 0.9411 (m100) cc_final: 0.8755 (m100) REVERT: B 670 MET cc_start: 0.9191 (mtp) cc_final: 0.8616 (mmt) REVERT: B 760 ASP cc_start: 0.9077 (m-30) cc_final: 0.8877 (p0) REVERT: B 807 MET cc_start: 0.9651 (mmp) cc_final: 0.9403 (mmm) REVERT: C 85 ILE cc_start: 0.8953 (mm) cc_final: 0.8678 (tp) REVERT: C 267 GLU cc_start: 0.9203 (tt0) cc_final: 0.8902 (tm-30) REVERT: C 361 MET cc_start: 0.7900 (mmm) cc_final: 0.7507 (tpp) REVERT: C 408 MET cc_start: 0.7828 (mmp) cc_final: 0.7517 (mmm) REVERT: C 427 ASP cc_start: 0.8993 (m-30) cc_final: 0.8672 (m-30) REVERT: C 517 PHE cc_start: 0.8955 (t80) cc_final: 0.8445 (t80) REVERT: C 527 MET cc_start: 0.8711 (ptm) cc_final: 0.8506 (ppp) REVERT: C 528 CYS cc_start: 0.9805 (m) cc_final: 0.8676 (m) REVERT: C 659 PHE cc_start: 0.9524 (m-80) cc_final: 0.9129 (m-80) REVERT: C 721 MET cc_start: 0.9351 (ptm) cc_final: 0.9074 (ppp) REVERT: C 723 VAL cc_start: 0.8784 (m) cc_final: 0.8491 (m) REVERT: D 126 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 159 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 221 ILE cc_start: 0.8878 (mt) cc_final: 0.8644 (mm) REVERT: D 361 MET cc_start: 0.7602 (mmm) cc_final: 0.6675 (mmm) REVERT: D 424 TYR cc_start: 0.7661 (t80) cc_final: 0.6941 (t80) REVERT: D 521 LEU cc_start: 0.9134 (tt) cc_final: 0.8848 (tp) REVERT: D 710 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8854 (tt0) REVERT: D 807 MET cc_start: 0.9683 (mmp) cc_final: 0.9413 (mmm) REVERT: E 121 LYS cc_start: 0.9418 (mttt) cc_final: 0.9005 (tmtt) REVERT: E 146 CYS cc_start: 0.7172 (m) cc_final: 0.6650 (t) REVERT: E 220 MET cc_start: 0.9459 (mmp) cc_final: 0.9132 (mmm) REVERT: F 121 LYS cc_start: 0.9422 (mttt) cc_final: 0.8997 (tmtt) REVERT: F 146 CYS cc_start: 0.7421 (m) cc_final: 0.6929 (t) REVERT: F 164 PHE cc_start: 0.8867 (m-80) cc_final: 0.8467 (m-80) outliers start: 3 outliers final: 0 residues processed: 421 average time/residue: 0.1766 time to fit residues: 121.2024 Evaluate side-chains 279 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 15 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 121 optimal weight: 0.0170 chunk 203 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 229 optimal weight: 7.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 791 ASN B 46 HIS B 65 GLN B 147 GLN B 246 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 214 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN D 147 GLN D 246 GLN D 344 ASN D 412 HIS F 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.035961 restraints weight = 202365.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.037194 restraints weight = 124989.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.038053 restraints weight = 88703.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.038670 restraints weight = 69138.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039113 restraints weight = 57430.749| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28172 Z= 0.128 Angle : 0.556 8.332 38108 Z= 0.296 Chirality : 0.040 0.205 4236 Planarity : 0.005 0.088 4768 Dihedral : 5.218 67.081 3934 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 0.10 % Allowed : 1.59 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3452 helix: 1.33 (0.13), residues: 1691 sheet: -1.81 (0.25), residues: 395 loop : -0.11 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 599 TYR 0.021 0.001 TYR B 450 PHE 0.022 0.002 PHE C 623 TRP 0.024 0.002 TRP E 198 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00269 (28162) covalent geometry : angle 0.55379 (38088) SS BOND : bond 0.00311 ( 10) SS BOND : angle 2.07653 ( 20) hydrogen bonds : bond 0.03493 ( 1381) hydrogen bonds : angle 4.94099 ( 3987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 367 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 129 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8810 (pp30) REVERT: A 161 THR cc_start: 0.8676 (m) cc_final: 0.8332 (p) REVERT: A 194 LEU cc_start: 0.9590 (tp) cc_final: 0.9201 (tp) REVERT: A 407 MET cc_start: 0.8076 (mtm) cc_final: 0.7815 (mpp) REVERT: A 408 MET cc_start: 0.8293 (mmm) cc_final: 0.8050 (mmm) REVERT: A 414 MET cc_start: 0.9096 (tpp) cc_final: 0.8806 (tpp) REVERT: A 427 ASP cc_start: 0.9016 (m-30) cc_final: 0.8627 (m-30) REVERT: A 463 MET cc_start: 0.9063 (mtp) cc_final: 0.8846 (mmm) REVERT: A 511 LYS cc_start: 0.8803 (mttt) cc_final: 0.8453 (mmmt) REVERT: A 608 PHE cc_start: 0.9056 (t80) cc_final: 0.8823 (t80) REVERT: A 638 ASP cc_start: 0.9325 (m-30) cc_final: 0.9085 (m-30) REVERT: A 670 MET cc_start: 0.8751 (mmm) cc_final: 0.8246 (mmm) REVERT: A 807 MET cc_start: 0.9403 (mmp) cc_final: 0.8780 (mtt) REVERT: B 93 HIS cc_start: 0.8439 (m90) cc_final: 0.8218 (m90) REVERT: B 245 PHE cc_start: 0.8043 (m-80) cc_final: 0.7773 (m-10) REVERT: B 361 MET cc_start: 0.7505 (mmm) cc_final: 0.7122 (tpp) REVERT: B 408 MET cc_start: 0.6798 (mmm) cc_final: 0.6052 (mmm) REVERT: B 517 PHE cc_start: 0.9236 (t80) cc_final: 0.8900 (t80) REVERT: B 521 LEU cc_start: 0.9164 (tt) cc_final: 0.8757 (tp) REVERT: B 526 TRP cc_start: 0.9445 (m100) cc_final: 0.9208 (m100) REVERT: C 85 ILE cc_start: 0.9088 (mm) cc_final: 0.8831 (tp) REVERT: C 194 LEU cc_start: 0.9711 (tp) cc_final: 0.9290 (tp) REVERT: C 267 GLU cc_start: 0.9201 (tt0) cc_final: 0.8905 (tm-30) REVERT: C 361 MET cc_start: 0.8204 (mmm) cc_final: 0.7656 (mmm) REVERT: C 424 TYR cc_start: 0.8791 (t80) cc_final: 0.8445 (t80) REVERT: C 427 ASP cc_start: 0.9063 (m-30) cc_final: 0.8694 (m-30) REVERT: C 527 MET cc_start: 0.9269 (ptm) cc_final: 0.8963 (ppp) REVERT: C 528 CYS cc_start: 0.9717 (m) cc_final: 0.9069 (m) REVERT: C 659 PHE cc_start: 0.9569 (m-80) cc_final: 0.9251 (m-80) REVERT: C 670 MET cc_start: 0.8782 (mmt) cc_final: 0.8500 (mmp) REVERT: C 704 LEU cc_start: 0.7735 (tp) cc_final: 0.7466 (tp) REVERT: C 721 MET cc_start: 0.9422 (ptm) cc_final: 0.8986 (ptm) REVERT: D 159 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7890 (tm-30) REVERT: D 221 ILE cc_start: 0.9159 (mt) cc_final: 0.8945 (mm) REVERT: D 361 MET cc_start: 0.7667 (mmm) cc_final: 0.6946 (mmt) REVERT: D 521 LEU cc_start: 0.8997 (tt) cc_final: 0.8609 (tp) REVERT: D 526 TRP cc_start: 0.9401 (m100) cc_final: 0.9141 (m100) REVERT: D 605 TRP cc_start: 0.9150 (t-100) cc_final: 0.8474 (t60) REVERT: D 710 GLU cc_start: 0.9502 (mt-10) cc_final: 0.8966 (tt0) REVERT: E 100 GLU cc_start: 0.8677 (tt0) cc_final: 0.8138 (tp30) REVERT: E 121 LYS cc_start: 0.9420 (mttt) cc_final: 0.8961 (tmtt) REVERT: E 146 CYS cc_start: 0.7300 (m) cc_final: 0.6885 (t) REVERT: E 220 MET cc_start: 0.9549 (mmp) cc_final: 0.9293 (mmm) REVERT: F 100 GLU cc_start: 0.8664 (tt0) cc_final: 0.8135 (tp30) REVERT: F 121 LYS cc_start: 0.9465 (mttt) cc_final: 0.9046 (tmtt) REVERT: F 146 CYS cc_start: 0.7472 (m) cc_final: 0.6947 (t) outliers start: 3 outliers final: 0 residues processed: 369 average time/residue: 0.1713 time to fit residues: 103.5535 Evaluate side-chains 261 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 103 optimal weight: 0.0060 chunk 279 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 99 optimal weight: 0.0040 chunk 59 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.036133 restraints weight = 198833.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037359 restraints weight = 124119.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038223 restraints weight = 88703.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.038840 restraints weight = 69463.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039293 restraints weight = 57917.828| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28172 Z= 0.101 Angle : 0.520 8.124 38108 Z= 0.270 Chirality : 0.039 0.182 4236 Planarity : 0.004 0.065 4768 Dihedral : 4.937 65.295 3934 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.53 % Favored : 96.09 % Rotamer: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3452 helix: 1.61 (0.13), residues: 1687 sheet: -1.57 (0.25), residues: 400 loop : -0.18 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.016 0.001 TYR A 616 PHE 0.021 0.001 PHE A 623 TRP 0.021 0.001 TRP A 262 HIS 0.005 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00217 (28162) covalent geometry : angle 0.51815 (38088) SS BOND : bond 0.00189 ( 10) SS BOND : angle 1.82744 ( 20) hydrogen bonds : bond 0.03124 ( 1381) hydrogen bonds : angle 4.61163 ( 3987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 347 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8820 (pp30) REVERT: A 161 THR cc_start: 0.8736 (m) cc_final: 0.8374 (p) REVERT: A 194 LEU cc_start: 0.9650 (tp) cc_final: 0.9354 (tp) REVERT: A 407 MET cc_start: 0.8051 (mtm) cc_final: 0.7724 (mpp) REVERT: A 408 MET cc_start: 0.8261 (mmm) cc_final: 0.7866 (mmm) REVERT: A 427 ASP cc_start: 0.8990 (m-30) cc_final: 0.8575 (m-30) REVERT: A 463 MET cc_start: 0.9046 (mtp) cc_final: 0.8735 (mmm) REVERT: A 496 MET cc_start: 0.8701 (mmp) cc_final: 0.8452 (mmm) REVERT: A 511 LYS cc_start: 0.8819 (mttt) cc_final: 0.8420 (mmmt) REVERT: A 674 MET cc_start: 0.9205 (ttm) cc_final: 0.8480 (mmm) REVERT: B 93 HIS cc_start: 0.8257 (m90) cc_final: 0.8039 (m90) REVERT: B 361 MET cc_start: 0.7545 (mmm) cc_final: 0.7283 (tpp) REVERT: B 408 MET cc_start: 0.6984 (mmm) cc_final: 0.6332 (mmm) REVERT: B 412 HIS cc_start: 0.8700 (p-80) cc_final: 0.8476 (p-80) REVERT: B 463 MET cc_start: 0.8185 (pmm) cc_final: 0.7896 (pmm) REVERT: B 521 LEU cc_start: 0.9072 (tt) cc_final: 0.8625 (tp) REVERT: B 526 TRP cc_start: 0.9437 (m100) cc_final: 0.9198 (m100) REVERT: B 807 MET cc_start: 0.9650 (mmp) cc_final: 0.9407 (mmm) REVERT: C 14 ILE cc_start: 0.9560 (pt) cc_final: 0.9232 (mm) REVERT: C 267 GLU cc_start: 0.9223 (tt0) cc_final: 0.8902 (tm-30) REVERT: C 361 MET cc_start: 0.8109 (mmm) cc_final: 0.7576 (mmm) REVERT: C 424 TYR cc_start: 0.8795 (t80) cc_final: 0.8445 (t80) REVERT: C 427 ASP cc_start: 0.9083 (m-30) cc_final: 0.8643 (m-30) REVERT: C 496 MET cc_start: 0.8727 (mmm) cc_final: 0.8422 (mmm) REVERT: C 659 PHE cc_start: 0.9556 (m-80) cc_final: 0.9274 (m-80) REVERT: C 670 MET cc_start: 0.9014 (mmt) cc_final: 0.8577 (mmm) REVERT: C 704 LEU cc_start: 0.7728 (tp) cc_final: 0.7428 (tp) REVERT: C 789 LEU cc_start: 0.9214 (pp) cc_final: 0.9008 (mp) REVERT: D 159 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7957 (tm-30) REVERT: D 221 ILE cc_start: 0.9222 (mt) cc_final: 0.8993 (mm) REVERT: D 361 MET cc_start: 0.7878 (mmm) cc_final: 0.7214 (mmt) REVERT: D 380 MET cc_start: 0.9068 (ttm) cc_final: 0.8685 (mtp) REVERT: D 521 LEU cc_start: 0.8960 (tt) cc_final: 0.8540 (tp) REVERT: D 526 TRP cc_start: 0.9369 (m100) cc_final: 0.9128 (m100) REVERT: D 605 TRP cc_start: 0.9237 (t-100) cc_final: 0.8724 (t60) REVERT: D 617 THR cc_start: 0.9268 (m) cc_final: 0.8974 (p) REVERT: D 670 MET cc_start: 0.9387 (ttm) cc_final: 0.8776 (mmm) REVERT: D 710 GLU cc_start: 0.9477 (mt-10) cc_final: 0.8962 (tt0) REVERT: D 807 MET cc_start: 0.9694 (mmp) cc_final: 0.9493 (mmm) REVERT: E 100 GLU cc_start: 0.8693 (tt0) cc_final: 0.8133 (tp30) REVERT: E 121 LYS cc_start: 0.9456 (mttt) cc_final: 0.9039 (tmtt) REVERT: E 146 CYS cc_start: 0.7314 (m) cc_final: 0.6850 (t) REVERT: E 220 MET cc_start: 0.9557 (mmp) cc_final: 0.9305 (mmm) REVERT: F 100 GLU cc_start: 0.8681 (tt0) cc_final: 0.8144 (tp30) REVERT: F 121 LYS cc_start: 0.9460 (mttt) cc_final: 0.8981 (tmtt) REVERT: F 146 CYS cc_start: 0.7428 (m) cc_final: 0.6916 (t) outliers start: 2 outliers final: 1 residues processed: 347 average time/residue: 0.1668 time to fit residues: 95.8794 Evaluate side-chains 249 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 28 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 110 optimal weight: 0.2980 chunk 266 optimal weight: 0.0060 chunk 241 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 2.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 46 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN C 311 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN F 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.045403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034212 restraints weight = 210521.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035343 restraints weight = 134010.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036150 restraints weight = 97103.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036715 restraints weight = 76943.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037092 restraints weight = 64843.400| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28172 Z= 0.173 Angle : 0.604 8.377 38108 Z= 0.320 Chirality : 0.041 0.175 4236 Planarity : 0.005 0.063 4768 Dihedral : 5.132 63.399 3934 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.32 % Favored : 95.31 % Rotamer: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3452 helix: 1.55 (0.13), residues: 1695 sheet: -1.38 (0.26), residues: 380 loop : -0.20 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 303 TYR 0.018 0.002 TYR C 218 PHE 0.055 0.002 PHE A 584 TRP 0.032 0.002 TRP A 323 HIS 0.012 0.002 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00371 (28162) covalent geometry : angle 0.60332 (38088) SS BOND : bond 0.00244 ( 10) SS BOND : angle 1.75300 ( 20) hydrogen bonds : bond 0.03569 ( 1381) hydrogen bonds : angle 4.76807 ( 3987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8564 (mtm) cc_final: 0.8281 (mpp) REVERT: A 408 MET cc_start: 0.8501 (mmm) cc_final: 0.8263 (mmm) REVERT: A 427 ASP cc_start: 0.9200 (m-30) cc_final: 0.8795 (m-30) REVERT: A 463 MET cc_start: 0.9234 (mtp) cc_final: 0.8802 (mmm) REVERT: A 511 LYS cc_start: 0.8853 (mttt) cc_final: 0.8582 (mmmt) REVERT: A 526 TRP cc_start: 0.9303 (m100) cc_final: 0.8938 (m100) REVERT: A 627 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8770 (mt-10) REVERT: A 638 ASP cc_start: 0.9380 (m-30) cc_final: 0.9175 (m-30) REVERT: A 674 MET cc_start: 0.9229 (ttm) cc_final: 0.8842 (mmm) REVERT: A 721 MET cc_start: 0.9282 (ptm) cc_final: 0.9080 (ptt) REVERT: B 79 LYS cc_start: 0.9401 (pttp) cc_final: 0.8774 (pttm) REVERT: B 89 CYS cc_start: 0.8570 (m) cc_final: 0.8359 (m) REVERT: B 235 ILE cc_start: 0.9795 (pt) cc_final: 0.9497 (mm) REVERT: B 407 MET cc_start: 0.9148 (mmp) cc_final: 0.8933 (mmm) REVERT: B 408 MET cc_start: 0.7334 (mmm) cc_final: 0.6686 (mmm) REVERT: B 412 HIS cc_start: 0.8843 (p-80) cc_final: 0.8624 (p-80) REVERT: B 521 LEU cc_start: 0.8989 (tt) cc_final: 0.8059 (tp) REVERT: B 526 TRP cc_start: 0.9471 (m100) cc_final: 0.8729 (m100) REVERT: C 88 PHE cc_start: 0.8931 (m-80) cc_final: 0.8536 (m-80) REVERT: C 361 MET cc_start: 0.8312 (mmm) cc_final: 0.7836 (mmm) REVERT: C 427 ASP cc_start: 0.9247 (m-30) cc_final: 0.8824 (m-30) REVERT: C 463 MET cc_start: 0.9518 (mmt) cc_final: 0.9021 (tpp) REVERT: C 527 MET cc_start: 0.9080 (ppp) cc_final: 0.8864 (ppp) REVERT: C 659 PHE cc_start: 0.9575 (m-80) cc_final: 0.9292 (m-80) REVERT: C 674 MET cc_start: 0.9531 (mtm) cc_final: 0.8598 (mmm) REVERT: D 159 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 235 ILE cc_start: 0.9789 (pt) cc_final: 0.9449 (tp) REVERT: D 380 MET cc_start: 0.9274 (ttm) cc_final: 0.8640 (mtp) REVERT: D 408 MET cc_start: 0.7737 (mmm) cc_final: 0.7445 (tpp) REVERT: D 604 VAL cc_start: 0.9356 (t) cc_final: 0.9106 (p) REVERT: D 605 TRP cc_start: 0.9442 (t-100) cc_final: 0.8752 (t60) REVERT: D 609 THR cc_start: 0.9557 (t) cc_final: 0.9314 (p) REVERT: D 670 MET cc_start: 0.9450 (ttm) cc_final: 0.8981 (ttm) REVERT: E 100 GLU cc_start: 0.8714 (tt0) cc_final: 0.8078 (tp30) REVERT: E 121 LYS cc_start: 0.9473 (mttt) cc_final: 0.8988 (tmtt) REVERT: E 146 CYS cc_start: 0.7568 (m) cc_final: 0.7068 (t) REVERT: E 182 MET cc_start: 0.9315 (mmp) cc_final: 0.9081 (mmm) REVERT: E 220 MET cc_start: 0.9664 (mmp) cc_final: 0.9300 (mmm) REVERT: F 100 GLU cc_start: 0.8694 (tt0) cc_final: 0.8072 (tp30) REVERT: F 121 LYS cc_start: 0.9485 (mttt) cc_final: 0.9053 (tmtt) REVERT: F 146 CYS cc_start: 0.7642 (m) cc_final: 0.7325 (t) REVERT: F 181 MET cc_start: 0.9784 (mmm) cc_final: 0.9459 (mmm) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1757 time to fit residues: 82.6729 Evaluate side-chains 215 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 164 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN E 188 GLN F 33 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034459 restraints weight = 207233.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035657 restraints weight = 129204.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.036490 restraints weight = 92444.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037080 restraints weight = 72664.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037464 restraints weight = 60957.875| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28172 Z= 0.116 Angle : 0.528 8.520 38108 Z= 0.275 Chirality : 0.039 0.195 4236 Planarity : 0.004 0.063 4768 Dihedral : 4.866 61.651 3934 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.77 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3452 helix: 1.82 (0.13), residues: 1703 sheet: -1.36 (0.25), residues: 402 loop : -0.24 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.014 0.001 TYR C 77 PHE 0.023 0.001 PHE A 584 TRP 0.037 0.001 TRP F 31 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00257 (28162) covalent geometry : angle 0.52701 (38088) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.78117 ( 20) hydrogen bonds : bond 0.03182 ( 1381) hydrogen bonds : angle 4.47446 ( 3987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8541 (mmm) cc_final: 0.8336 (mmm) REVERT: A 427 ASP cc_start: 0.9239 (m-30) cc_final: 0.8800 (m-30) REVERT: A 463 MET cc_start: 0.9337 (mtp) cc_final: 0.8928 (mmm) REVERT: A 496 MET cc_start: 0.8912 (mmm) cc_final: 0.8672 (mmm) REVERT: A 511 LYS cc_start: 0.8874 (mttt) cc_final: 0.8603 (mmmt) REVERT: A 526 TRP cc_start: 0.9324 (m100) cc_final: 0.8981 (m100) REVERT: A 674 MET cc_start: 0.9266 (ttm) cc_final: 0.8915 (mmm) REVERT: A 721 MET cc_start: 0.9310 (ptm) cc_final: 0.9042 (ptm) REVERT: B 25 GLU cc_start: 0.9047 (mp0) cc_final: 0.8586 (mm-30) REVERT: B 79 LYS cc_start: 0.9309 (pttp) cc_final: 0.9023 (pttt) REVERT: B 235 ILE cc_start: 0.9810 (pt) cc_final: 0.9581 (mm) REVERT: B 292 MET cc_start: 0.9134 (ptp) cc_final: 0.8907 (ptt) REVERT: B 361 MET cc_start: 0.8715 (mmm) cc_final: 0.8156 (tpp) REVERT: B 380 MET cc_start: 0.9094 (ttm) cc_final: 0.8604 (mtp) REVERT: B 384 GLU cc_start: 0.8917 (tp30) cc_final: 0.8709 (tp30) REVERT: B 408 MET cc_start: 0.7253 (mmm) cc_final: 0.6609 (mmm) REVERT: B 412 HIS cc_start: 0.8842 (p-80) cc_final: 0.8612 (p-80) REVERT: B 521 LEU cc_start: 0.8917 (tt) cc_final: 0.7971 (tp) REVERT: B 526 TRP cc_start: 0.9506 (m100) cc_final: 0.8838 (m100) REVERT: B 659 PHE cc_start: 0.9424 (m-80) cc_final: 0.9108 (m-80) REVERT: C 88 PHE cc_start: 0.9044 (m-80) cc_final: 0.8759 (m-80) REVERT: C 408 MET cc_start: 0.8485 (mmp) cc_final: 0.7756 (mmm) REVERT: C 424 TYR cc_start: 0.9318 (t80) cc_final: 0.8849 (t80) REVERT: C 526 TRP cc_start: 0.9355 (m100) cc_final: 0.8915 (m100) REVERT: C 527 MET cc_start: 0.9048 (ppp) cc_final: 0.8740 (ppp) REVERT: C 608 PHE cc_start: 0.9133 (t80) cc_final: 0.8837 (t80) REVERT: C 638 ASP cc_start: 0.9357 (m-30) cc_final: 0.9138 (m-30) REVERT: C 670 MET cc_start: 0.9456 (mmp) cc_final: 0.9214 (mmm) REVERT: C 674 MET cc_start: 0.9487 (mtm) cc_final: 0.8819 (mmm) REVERT: C 704 LEU cc_start: 0.8635 (tp) cc_final: 0.8412 (tp) REVERT: D 25 GLU cc_start: 0.9074 (mp0) cc_final: 0.8703 (mm-30) REVERT: D 159 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 235 ILE cc_start: 0.9798 (pt) cc_final: 0.9509 (tp) REVERT: D 361 MET cc_start: 0.8685 (mmp) cc_final: 0.7935 (tpp) REVERT: D 380 MET cc_start: 0.9125 (ttm) cc_final: 0.8855 (mtp) REVERT: D 408 MET cc_start: 0.8031 (mmm) cc_final: 0.7208 (mmm) REVERT: D 412 HIS cc_start: 0.8479 (p90) cc_final: 0.7756 (p90) REVERT: D 526 TRP cc_start: 0.9417 (m100) cc_final: 0.8473 (m100) REVERT: D 604 VAL cc_start: 0.9334 (t) cc_final: 0.9092 (p) REVERT: D 605 TRP cc_start: 0.9452 (t-100) cc_final: 0.8849 (t60) REVERT: D 659 PHE cc_start: 0.9308 (m-80) cc_final: 0.8912 (m-80) REVERT: E 100 GLU cc_start: 0.8741 (tt0) cc_final: 0.8072 (tp30) REVERT: E 121 LYS cc_start: 0.9411 (mttt) cc_final: 0.8919 (tmtt) REVERT: E 146 CYS cc_start: 0.7415 (m) cc_final: 0.6982 (t) REVERT: E 182 MET cc_start: 0.9297 (mmp) cc_final: 0.9064 (mmm) REVERT: E 220 MET cc_start: 0.9662 (mmp) cc_final: 0.9279 (mmm) REVERT: F 100 GLU cc_start: 0.8703 (tt0) cc_final: 0.8040 (tp30) REVERT: F 121 LYS cc_start: 0.9458 (mttt) cc_final: 0.8983 (tmtt) REVERT: F 146 CYS cc_start: 0.7584 (m) cc_final: 0.7203 (t) REVERT: F 168 PHE cc_start: 0.8397 (m-80) cc_final: 0.8019 (m-80) REVERT: F 181 MET cc_start: 0.9743 (mmm) cc_final: 0.9448 (mpp) REVERT: F 204 ASP cc_start: 0.8458 (t0) cc_final: 0.8230 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1655 time to fit residues: 79.4646 Evaluate side-chains 220 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 183 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 249 optimal weight: 0.0050 overall best weight: 2.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 337 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 182 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 180 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033256 restraints weight = 209196.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034385 restraints weight = 131668.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035182 restraints weight = 94488.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.035743 restraints weight = 74487.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036113 restraints weight = 62676.144| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.7365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28172 Z= 0.187 Angle : 0.609 10.220 38108 Z= 0.321 Chirality : 0.040 0.193 4236 Planarity : 0.005 0.069 4768 Dihedral : 5.088 59.476 3934 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3452 helix: 1.68 (0.13), residues: 1693 sheet: -1.40 (0.25), residues: 408 loop : -0.25 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 599 TYR 0.015 0.002 TYR C 77 PHE 0.030 0.002 PHE F 21 TRP 0.044 0.002 TRP A 605 HIS 0.013 0.002 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00396 (28162) covalent geometry : angle 0.60795 (38088) SS BOND : bond 0.00245 ( 10) SS BOND : angle 1.86062 ( 20) hydrogen bonds : bond 0.03500 ( 1381) hydrogen bonds : angle 4.73360 ( 3987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8860 (mmm) cc_final: 0.8471 (mmm) REVERT: A 463 MET cc_start: 0.9364 (mtp) cc_final: 0.8884 (mmm) REVERT: A 496 MET cc_start: 0.9078 (mmm) cc_final: 0.8552 (mmm) REVERT: A 526 TRP cc_start: 0.9285 (m100) cc_final: 0.8820 (m100) REVERT: A 674 MET cc_start: 0.9399 (ttm) cc_final: 0.8960 (mmm) REVERT: A 721 MET cc_start: 0.9324 (ptm) cc_final: 0.9085 (ptm) REVERT: A 807 MET cc_start: 0.9476 (mmp) cc_final: 0.9018 (mtt) REVERT: B 33 MET cc_start: 0.9146 (ppp) cc_final: 0.8812 (ptt) REVERT: B 79 LYS cc_start: 0.9425 (pttp) cc_final: 0.8879 (pttm) REVERT: B 89 CYS cc_start: 0.9043 (m) cc_final: 0.8826 (m) REVERT: B 292 MET cc_start: 0.9249 (ptp) cc_final: 0.9035 (ptt) REVERT: B 361 MET cc_start: 0.8958 (mmm) cc_final: 0.8626 (tpp) REVERT: B 407 MET cc_start: 0.9142 (mmp) cc_final: 0.8931 (mmm) REVERT: B 408 MET cc_start: 0.7676 (mmm) cc_final: 0.6932 (mmm) REVERT: B 659 PHE cc_start: 0.9330 (m-80) cc_final: 0.9032 (m-80) REVERT: C 88 PHE cc_start: 0.9162 (m-80) cc_final: 0.8889 (m-80) REVERT: C 113 MET cc_start: 0.9481 (mmp) cc_final: 0.9187 (mmp) REVERT: C 527 MET cc_start: 0.9100 (ppp) cc_final: 0.8892 (ppp) REVERT: C 670 MET cc_start: 0.9542 (mmp) cc_final: 0.9138 (mmm) REVERT: C 674 MET cc_start: 0.9575 (mtm) cc_final: 0.8758 (mmm) REVERT: C 704 LEU cc_start: 0.8966 (tp) cc_final: 0.8735 (tp) REVERT: C 708 MET cc_start: 0.9117 (mmp) cc_final: 0.8899 (mmm) REVERT: C 807 MET cc_start: 0.8934 (mtm) cc_final: 0.8667 (mmp) REVERT: D 159 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 235 ILE cc_start: 0.9861 (pt) cc_final: 0.9629 (tp) REVERT: D 361 MET cc_start: 0.8706 (mmp) cc_final: 0.8190 (mmp) REVERT: D 380 MET cc_start: 0.9140 (ttm) cc_final: 0.8863 (mtp) REVERT: D 407 MET cc_start: 0.9188 (mmp) cc_final: 0.8908 (mmm) REVERT: D 604 VAL cc_start: 0.9412 (t) cc_final: 0.9156 (p) REVERT: D 605 TRP cc_start: 0.9378 (t-100) cc_final: 0.8730 (t60) REVERT: D 659 PHE cc_start: 0.9372 (m-80) cc_final: 0.8942 (m-80) REVERT: D 670 MET cc_start: 0.9615 (ppp) cc_final: 0.9380 (ppp) REVERT: E 100 GLU cc_start: 0.8718 (tt0) cc_final: 0.8008 (tp30) REVERT: E 121 LYS cc_start: 0.9455 (mttt) cc_final: 0.8923 (tmtt) REVERT: E 146 CYS cc_start: 0.7580 (m) cc_final: 0.7083 (t) REVERT: E 182 MET cc_start: 0.9354 (mmp) cc_final: 0.9147 (mmm) REVERT: E 220 MET cc_start: 0.9627 (mmp) cc_final: 0.9235 (mmm) REVERT: F 21 PHE cc_start: 0.9323 (m-80) cc_final: 0.9112 (m-80) REVERT: F 100 GLU cc_start: 0.8671 (tt0) cc_final: 0.8005 (tp30) REVERT: F 121 LYS cc_start: 0.9431 (mttt) cc_final: 0.8939 (tmtt) REVERT: F 146 CYS cc_start: 0.7601 (m) cc_final: 0.7023 (t) REVERT: F 181 MET cc_start: 0.9685 (mmm) cc_final: 0.9398 (mmm) REVERT: F 204 ASP cc_start: 0.8686 (t0) cc_final: 0.8370 (m-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1743 time to fit residues: 70.0224 Evaluate side-chains 188 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 231 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN C 236 GLN C 246 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034400 restraints weight = 209332.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035579 restraints weight = 128768.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.036402 restraints weight = 91873.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036976 restraints weight = 72120.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037391 restraints weight = 60722.523| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.7623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 28172 Z= 0.108 Angle : 0.548 12.891 38108 Z= 0.282 Chirality : 0.040 0.209 4236 Planarity : 0.004 0.083 4768 Dihedral : 4.857 58.455 3934 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.91 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3452 helix: 1.77 (0.13), residues: 1703 sheet: -1.24 (0.25), residues: 402 loop : -0.27 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 198 TYR 0.015 0.001 TYR C 77 PHE 0.024 0.001 PHE F 21 TRP 0.027 0.001 TRP A 605 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00237 (28162) covalent geometry : angle 0.54739 (38088) SS BOND : bond 0.00168 ( 10) SS BOND : angle 1.60317 ( 20) hydrogen bonds : bond 0.03165 ( 1381) hydrogen bonds : angle 4.44221 ( 3987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9042 (m-80) cc_final: 0.8786 (m-80) REVERT: A 113 MET cc_start: 0.9473 (mmp) cc_final: 0.9247 (mmp) REVERT: A 178 ARG cc_start: 0.8964 (mtt90) cc_final: 0.8236 (tpp-160) REVERT: A 408 MET cc_start: 0.8909 (mmm) cc_final: 0.8316 (mmm) REVERT: A 463 MET cc_start: 0.9380 (mtp) cc_final: 0.9020 (mmt) REVERT: A 511 LYS cc_start: 0.8870 (mttt) cc_final: 0.8640 (mmmt) REVERT: A 526 TRP cc_start: 0.9265 (m100) cc_final: 0.8897 (m100) REVERT: A 674 MET cc_start: 0.9320 (ttm) cc_final: 0.9023 (mmm) REVERT: A 721 MET cc_start: 0.9296 (ptm) cc_final: 0.9033 (ptm) REVERT: B 25 GLU cc_start: 0.9149 (mp0) cc_final: 0.8650 (mm-30) REVERT: B 79 LYS cc_start: 0.9308 (pttp) cc_final: 0.8816 (pttm) REVERT: B 235 ILE cc_start: 0.9830 (pt) cc_final: 0.9590 (mm) REVERT: B 292 MET cc_start: 0.9268 (ptp) cc_final: 0.9057 (ptt) REVERT: B 361 MET cc_start: 0.8995 (mmm) cc_final: 0.8668 (tpp) REVERT: B 408 MET cc_start: 0.7537 (mmm) cc_final: 0.6786 (mmm) REVERT: B 585 MET cc_start: 0.6032 (mtt) cc_final: 0.5726 (mtp) REVERT: B 586 GLN cc_start: 0.6389 (pt0) cc_final: 0.5861 (pt0) REVERT: B 605 TRP cc_start: 0.9455 (t-100) cc_final: 0.8864 (t60) REVERT: B 659 PHE cc_start: 0.9364 (m-80) cc_final: 0.9037 (m-80) REVERT: C 88 PHE cc_start: 0.9172 (m-80) cc_final: 0.8912 (m-80) REVERT: C 89 CYS cc_start: 0.8659 (m) cc_final: 0.7815 (p) REVERT: C 113 MET cc_start: 0.9396 (mmp) cc_final: 0.9169 (mmp) REVERT: C 380 MET cc_start: 0.9214 (ppp) cc_final: 0.8878 (ppp) REVERT: C 408 MET cc_start: 0.8722 (mmp) cc_final: 0.8185 (mmm) REVERT: C 424 TYR cc_start: 0.9380 (t80) cc_final: 0.9006 (t80) REVERT: C 463 MET cc_start: 0.9640 (mmt) cc_final: 0.9397 (mmm) REVERT: C 521 LEU cc_start: 0.8364 (tp) cc_final: 0.8028 (tp) REVERT: C 527 MET cc_start: 0.9061 (ppp) cc_final: 0.8856 (ppp) REVERT: C 608 PHE cc_start: 0.9167 (t80) cc_final: 0.8780 (t80) REVERT: C 670 MET cc_start: 0.9498 (mmp) cc_final: 0.9190 (mmm) REVERT: C 674 MET cc_start: 0.9572 (mtm) cc_final: 0.8814 (mmm) REVERT: C 704 LEU cc_start: 0.8878 (tp) cc_final: 0.8643 (tp) REVERT: C 708 MET cc_start: 0.8967 (mmp) cc_final: 0.8763 (mmm) REVERT: C 807 MET cc_start: 0.8858 (mtm) cc_final: 0.8635 (mmp) REVERT: D 25 GLU cc_start: 0.9121 (mp0) cc_final: 0.8670 (mm-30) REVERT: D 159 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 235 ILE cc_start: 0.9860 (pt) cc_final: 0.9657 (tp) REVERT: D 361 MET cc_start: 0.8865 (mmp) cc_final: 0.8207 (mmp) REVERT: D 408 MET cc_start: 0.8211 (mmm) cc_final: 0.7579 (mmm) REVERT: D 412 HIS cc_start: 0.8612 (p90) cc_final: 0.7924 (p90) REVERT: D 604 VAL cc_start: 0.9420 (t) cc_final: 0.9162 (p) REVERT: D 605 TRP cc_start: 0.9352 (t-100) cc_final: 0.8737 (t60) REVERT: D 659 PHE cc_start: 0.9316 (m-80) cc_final: 0.8916 (m-80) REVERT: D 670 MET cc_start: 0.9579 (ppp) cc_final: 0.9336 (ppp) REVERT: E 100 GLU cc_start: 0.8706 (tt0) cc_final: 0.8001 (tp30) REVERT: E 121 LYS cc_start: 0.9436 (mttt) cc_final: 0.8913 (tmtt) REVERT: E 146 CYS cc_start: 0.7485 (m) cc_final: 0.7017 (t) REVERT: E 220 MET cc_start: 0.9602 (mmp) cc_final: 0.9239 (mmm) REVERT: F 21 PHE cc_start: 0.9241 (m-80) cc_final: 0.9008 (m-80) REVERT: F 100 GLU cc_start: 0.8683 (tt0) cc_final: 0.8010 (tp30) REVERT: F 121 LYS cc_start: 0.9448 (mttt) cc_final: 0.8965 (tmtt) REVERT: F 146 CYS cc_start: 0.7501 (m) cc_final: 0.7021 (t) REVERT: F 168 PHE cc_start: 0.8268 (m-80) cc_final: 0.7857 (m-80) REVERT: F 204 ASP cc_start: 0.8697 (t0) cc_final: 0.8365 (m-30) REVERT: F 205 TYR cc_start: 0.7768 (m-10) cc_final: 0.7553 (m-10) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1822 time to fit residues: 75.6624 Evaluate side-chains 207 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 136 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 204 optimal weight: 0.0770 chunk 249 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 overall best weight: 2.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033025 restraints weight = 214944.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034158 restraints weight = 133048.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.034945 restraints weight = 95287.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.035495 restraints weight = 75168.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035853 restraints weight = 63321.942| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28172 Z= 0.186 Angle : 0.609 11.403 38108 Z= 0.319 Chirality : 0.041 0.222 4236 Planarity : 0.005 0.070 4768 Dihedral : 5.119 58.204 3934 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.72 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3452 helix: 1.57 (0.13), residues: 1703 sheet: -1.14 (0.26), residues: 370 loop : -0.35 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 198 TYR 0.014 0.001 TYR A 373 PHE 0.032 0.002 PHE A 584 TRP 0.015 0.001 TRP B 606 HIS 0.010 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00393 (28162) covalent geometry : angle 0.60786 (38088) SS BOND : bond 0.00724 ( 10) SS BOND : angle 1.88848 ( 20) hydrogen bonds : bond 0.03494 ( 1381) hydrogen bonds : angle 4.64663 ( 3987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9093 (m-80) cc_final: 0.8810 (m-80) REVERT: A 89 CYS cc_start: 0.8837 (m) cc_final: 0.8061 (p) REVERT: A 113 MET cc_start: 0.9567 (mmp) cc_final: 0.9227 (mmm) REVERT: A 463 MET cc_start: 0.9429 (mtp) cc_final: 0.8908 (mmm) REVERT: A 511 LYS cc_start: 0.8898 (mttt) cc_final: 0.8595 (mmmt) REVERT: A 526 TRP cc_start: 0.9304 (m100) cc_final: 0.8911 (m100) REVERT: A 629 MET cc_start: 0.8498 (mmp) cc_final: 0.8242 (mmm) REVERT: A 674 MET cc_start: 0.9366 (ttm) cc_final: 0.9051 (mmm) REVERT: A 708 MET cc_start: 0.8964 (mmp) cc_final: 0.8763 (mmm) REVERT: A 721 MET cc_start: 0.9310 (ptm) cc_final: 0.9006 (ptm) REVERT: A 807 MET cc_start: 0.9479 (mmp) cc_final: 0.9107 (mtt) REVERT: B 33 MET cc_start: 0.9171 (ppp) cc_final: 0.8838 (ptt) REVERT: B 79 LYS cc_start: 0.9455 (pttp) cc_final: 0.9101 (pttm) REVERT: B 235 ILE cc_start: 0.9850 (pt) cc_final: 0.9597 (mm) REVERT: B 361 MET cc_start: 0.9006 (mmm) cc_final: 0.8624 (tpp) REVERT: B 407 MET cc_start: 0.9113 (mmp) cc_final: 0.8842 (mmm) REVERT: B 408 MET cc_start: 0.7839 (mmm) cc_final: 0.7565 (mmm) REVERT: B 659 PHE cc_start: 0.9400 (m-80) cc_final: 0.9106 (m-80) REVERT: C 88 PHE cc_start: 0.9205 (m-80) cc_final: 0.8915 (m-80) REVERT: C 89 CYS cc_start: 0.8868 (m) cc_final: 0.8240 (p) REVERT: C 113 MET cc_start: 0.9506 (mmp) cc_final: 0.9105 (mmp) REVERT: C 380 MET cc_start: 0.9195 (ppp) cc_final: 0.8902 (ppp) REVERT: C 407 MET cc_start: 0.8107 (pmm) cc_final: 0.7865 (pmm) REVERT: C 408 MET cc_start: 0.8810 (mmp) cc_final: 0.8414 (mmm) REVERT: C 414 MET cc_start: 0.9331 (tpp) cc_final: 0.9102 (tpp) REVERT: C 463 MET cc_start: 0.9625 (mmt) cc_final: 0.9402 (mmm) REVERT: C 518 LEU cc_start: 0.9251 (mt) cc_final: 0.9035 (mp) REVERT: C 527 MET cc_start: 0.9091 (ppp) cc_final: 0.8877 (ppp) REVERT: C 670 MET cc_start: 0.9531 (mmp) cc_final: 0.9178 (mmm) REVERT: C 674 MET cc_start: 0.9583 (mtm) cc_final: 0.8827 (mmm) REVERT: C 708 MET cc_start: 0.9173 (mmp) cc_final: 0.8895 (mmm) REVERT: C 807 MET cc_start: 0.8895 (mtm) cc_final: 0.8687 (mmp) REVERT: D 159 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8057 (tm-30) REVERT: D 361 MET cc_start: 0.8690 (mmp) cc_final: 0.8087 (mmm) REVERT: D 407 MET cc_start: 0.9216 (mmp) cc_final: 0.8914 (mmm) REVERT: D 408 MET cc_start: 0.8395 (mmm) cc_final: 0.7648 (mmm) REVERT: D 412 HIS cc_start: 0.8637 (p90) cc_final: 0.7974 (p90) REVERT: D 604 VAL cc_start: 0.9470 (t) cc_final: 0.9226 (p) REVERT: D 605 TRP cc_start: 0.9360 (t-100) cc_final: 0.8660 (t60) REVERT: D 633 ILE cc_start: 0.9315 (pt) cc_final: 0.9083 (mp) REVERT: D 659 PHE cc_start: 0.9333 (m-80) cc_final: 0.8968 (m-80) REVERT: D 670 MET cc_start: 0.9594 (ppp) cc_final: 0.9365 (ppp) REVERT: D 708 MET cc_start: 0.9156 (mmp) cc_final: 0.8898 (mmm) REVERT: E 100 GLU cc_start: 0.8684 (tt0) cc_final: 0.7937 (tp30) REVERT: E 121 LYS cc_start: 0.9456 (mttt) cc_final: 0.8914 (tmtt) REVERT: E 146 CYS cc_start: 0.7608 (m) cc_final: 0.7169 (t) REVERT: E 182 MET cc_start: 0.9286 (mmp) cc_final: 0.9046 (mmm) REVERT: E 218 CYS cc_start: 0.8599 (m) cc_final: 0.8024 (t) REVERT: E 220 MET cc_start: 0.9598 (mmp) cc_final: 0.9240 (mmm) REVERT: F 21 PHE cc_start: 0.9278 (m-80) cc_final: 0.9076 (m-80) REVERT: F 100 GLU cc_start: 0.8610 (tt0) cc_final: 0.7894 (tp30) REVERT: F 121 LYS cc_start: 0.9466 (mttt) cc_final: 0.8952 (tmtt) REVERT: F 146 CYS cc_start: 0.7525 (m) cc_final: 0.6887 (t) REVERT: F 204 ASP cc_start: 0.8781 (t0) cc_final: 0.8395 (m-30) REVERT: F 205 TYR cc_start: 0.8016 (m-10) cc_final: 0.7787 (m-10) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1763 time to fit residues: 70.6841 Evaluate side-chains 192 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 70 optimal weight: 0.6980 chunk 217 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.045229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033897 restraints weight = 210080.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035078 restraints weight = 131821.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.035890 restraints weight = 94417.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.036463 restraints weight = 74398.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036835 restraints weight = 62675.246| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 28172 Z= 0.112 Angle : 0.555 9.564 38108 Z= 0.286 Chirality : 0.040 0.223 4236 Planarity : 0.004 0.080 4768 Dihedral : 4.863 57.434 3934 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.03 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3452 helix: 1.72 (0.13), residues: 1714 sheet: -1.13 (0.26), residues: 402 loop : -0.31 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 599 TYR 0.014 0.001 TYR C 616 PHE 0.026 0.001 PHE A 584 TRP 0.047 0.001 TRP A 605 HIS 0.010 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00248 (28162) covalent geometry : angle 0.55347 (38088) SS BOND : bond 0.00223 ( 10) SS BOND : angle 1.70801 ( 20) hydrogen bonds : bond 0.03135 ( 1381) hydrogen bonds : angle 4.41086 ( 3987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.098 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 88 PHE cc_start: 0.9094 (m-80) cc_final: 0.8794 (m-80) REVERT: A 89 CYS cc_start: 0.8813 (m) cc_final: 0.8001 (p) REVERT: A 113 MET cc_start: 0.9536 (mmp) cc_final: 0.9169 (mmp) REVERT: A 463 MET cc_start: 0.9428 (mtp) cc_final: 0.9051 (mmt) REVERT: A 496 MET cc_start: 0.8840 (mmm) cc_final: 0.8625 (mmm) REVERT: A 521 LEU cc_start: 0.8473 (tp) cc_final: 0.7482 (tp) REVERT: A 526 TRP cc_start: 0.9278 (m100) cc_final: 0.8813 (m100) REVERT: A 527 MET cc_start: 0.9472 (mtm) cc_final: 0.9182 (ptp) REVERT: A 629 MET cc_start: 0.8446 (mmp) cc_final: 0.8174 (mmm) REVERT: A 674 MET cc_start: 0.9280 (ttm) cc_final: 0.9070 (mmm) REVERT: A 721 MET cc_start: 0.9287 (ptm) cc_final: 0.8963 (ptm) REVERT: B 79 LYS cc_start: 0.9376 (pttp) cc_final: 0.8912 (pttm) REVERT: B 235 ILE cc_start: 0.9826 (pt) cc_final: 0.9617 (mm) REVERT: B 361 MET cc_start: 0.8991 (mmm) cc_final: 0.8610 (tpp) REVERT: B 605 TRP cc_start: 0.9404 (t-100) cc_final: 0.8989 (t60) REVERT: B 633 ILE cc_start: 0.9274 (pt) cc_final: 0.9068 (mp) REVERT: B 659 PHE cc_start: 0.9363 (m-80) cc_final: 0.9080 (m-80) REVERT: C 88 PHE cc_start: 0.9204 (m-80) cc_final: 0.8948 (m-80) REVERT: C 89 CYS cc_start: 0.8858 (m) cc_final: 0.8076 (p) REVERT: C 113 MET cc_start: 0.9413 (mmp) cc_final: 0.9145 (mmp) REVERT: C 380 MET cc_start: 0.9132 (ppp) cc_final: 0.8843 (ppp) REVERT: C 407 MET cc_start: 0.8081 (pmm) cc_final: 0.7865 (pmm) REVERT: C 408 MET cc_start: 0.8957 (mmp) cc_final: 0.8513 (mmm) REVERT: C 424 TYR cc_start: 0.9450 (t80) cc_final: 0.9235 (t80) REVERT: C 521 LEU cc_start: 0.8322 (tp) cc_final: 0.7979 (tp) REVERT: C 527 MET cc_start: 0.9112 (ppp) cc_final: 0.8888 (ppp) REVERT: C 670 MET cc_start: 0.9479 (mmp) cc_final: 0.9181 (mmm) REVERT: C 674 MET cc_start: 0.9560 (mtm) cc_final: 0.8957 (mmm) REVERT: C 704 LEU cc_start: 0.9055 (tp) cc_final: 0.8745 (tt) REVERT: C 708 MET cc_start: 0.9110 (mmp) cc_final: 0.8777 (mmm) REVERT: C 721 MET cc_start: 0.8717 (pmm) cc_final: 0.8113 (pmm) REVERT: C 807 MET cc_start: 0.8874 (mtm) cc_final: 0.8669 (mmp) REVERT: D 25 GLU cc_start: 0.9146 (mp0) cc_final: 0.8900 (mp0) REVERT: D 159 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 361 MET cc_start: 0.8729 (mmp) cc_final: 0.8123 (mmm) REVERT: D 408 MET cc_start: 0.8330 (mmm) cc_final: 0.7574 (mmm) REVERT: D 412 HIS cc_start: 0.8602 (p90) cc_final: 0.7884 (p90) REVERT: D 605 TRP cc_start: 0.9348 (t-100) cc_final: 0.8683 (t60) REVERT: D 633 ILE cc_start: 0.9300 (pt) cc_final: 0.9077 (mp) REVERT: D 659 PHE cc_start: 0.9292 (m-80) cc_final: 0.8908 (m-80) REVERT: E 100 GLU cc_start: 0.8721 (tt0) cc_final: 0.7971 (tp30) REVERT: E 121 LYS cc_start: 0.9428 (mttt) cc_final: 0.8875 (tmtt) REVERT: E 146 CYS cc_start: 0.7484 (m) cc_final: 0.6992 (t) REVERT: E 182 MET cc_start: 0.9247 (mmp) cc_final: 0.8992 (mmm) REVERT: E 218 CYS cc_start: 0.8538 (m) cc_final: 0.8003 (t) REVERT: E 220 MET cc_start: 0.9593 (mmp) cc_final: 0.9287 (mmm) REVERT: F 21 PHE cc_start: 0.9207 (m-80) cc_final: 0.8945 (m-80) REVERT: F 100 GLU cc_start: 0.8711 (tt0) cc_final: 0.7994 (tp30) REVERT: F 121 LYS cc_start: 0.9431 (mttt) cc_final: 0.8902 (tmtt) REVERT: F 146 CYS cc_start: 0.7464 (m) cc_final: 0.7065 (t) REVERT: F 204 ASP cc_start: 0.8734 (t0) cc_final: 0.8341 (m-30) REVERT: F 205 TYR cc_start: 0.7777 (m-10) cc_final: 0.7568 (m-10) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1704 time to fit residues: 71.8531 Evaluate side-chains 201 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 24 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033535 restraints weight = 211335.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.034697 restraints weight = 132567.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.035495 restraints weight = 95207.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.036068 restraints weight = 75294.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036432 restraints weight = 63441.071| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.8890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28172 Z= 0.130 Angle : 0.557 11.960 38108 Z= 0.288 Chirality : 0.040 0.217 4236 Planarity : 0.004 0.069 4768 Dihedral : 4.851 58.166 3934 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.46 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3452 helix: 1.76 (0.13), residues: 1714 sheet: -1.14 (0.27), residues: 360 loop : -0.38 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 198 TYR 0.017 0.001 TYR B 711 PHE 0.023 0.001 PHE F 21 TRP 0.018 0.001 TRP A 262 HIS 0.008 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00285 (28162) covalent geometry : angle 0.55500 (38088) SS BOND : bond 0.00248 ( 10) SS BOND : angle 1.89774 ( 20) hydrogen bonds : bond 0.03128 ( 1381) hydrogen bonds : angle 4.40165 ( 3987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.95 seconds wall clock time: 70 minutes 5.28 seconds (4205.28 seconds total)