Starting phenix.real_space_refine on Mon Sep 14 03:28:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_8687.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_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_8687/09_2026/5vhy_8687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_8687.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_8687.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_8687.cif" model { file = "/net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_8687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vhy_8687/09_2026/5vhy_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): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 chiralities: 1 Time building chain proxies: 5.62, per 1000 atoms: 0.20 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: 2.20 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: 1.07 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: 5.60 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 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: 16224 16.27 - 32.54: 279 32.54 - 48.82: 92 48.82 - 65.09: 14 65.09 - 81.36: 15 Dihedral angle restraints: 16624 sinusoidal: 6600 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 16621 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: 0.03 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.790 Find NCS groups from input model: 0.790 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 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 : 8.346 81.359 10186 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/Z covalent geometry : bond 0.00743 / 0.45 (28162) covalent geometry : angle 1.11992 / 0.78 (38088) SS BOND : bond 0.00201 / 0.12 ( 10) SS BOND : angle 25.89950 / 19.22 ( 20) hydrogen bonds : bond 0.17392 / 11.22 ( 1381) hydrogen bonds : angle 8.64972 / 6.18 ( 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 : 1.380 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: 0.1927 time to fit residues: 190.5405 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 : 1.083 ------------------------------------------------------------------------------- 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... A 24 GLN 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 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 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 228 ASN F 36 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.048217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036788 restraints weight = 203036.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.038034 restraints weight = 124262.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.038906 restraints weight = 87995.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.039504 restraints weight = 68547.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039971 restraints weight = 57168.522| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28172 Z= 0.140 Angle : 0.633 9.639 38108 Z= 0.334 Chirality : 0.042 0.228 4236 Planarity : 0.005 0.078 4768 Dihedral : 5.625 74.993 3794 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.62 % Favored : 95.77 % Rotamer: Outliers : 0.13 % Allowed : 1.45 % Favored : 98.41 % 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: -0.09 (0.14), residues: 3452 helix: 0.50 (0.12), residues: 1670 sheet: -1.98 (0.26), residues: 374 loop : 0.05 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 178 TYR 0.027 0.002 TYR B 450 PHE 0.028 0.002 PHE A 541 TRP 0.021 0.002 TRP C 766 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (28162) covalent geometry : angle 0.62818 / 0.33 (38088) SS BOND : bond 0.00401 / 0.20 ( 10) SS BOND : angle 3.60328 / 2.38 ( 20) hydrogen bonds : bond 0.04107 / 2.74 ( 1381) hydrogen bonds : angle 5.50440 / 3.86 ( 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 425 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 1.006 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 85 ILE cc_start: 0.8902 (mm) cc_final: 0.8597 (tp) REVERT: A 129 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8819 (pp30) REVERT: A 161 THR cc_start: 0.8539 (m) cc_final: 0.7892 (p) REVERT: A 260 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8522 (tm-30) REVERT: A 365 THR cc_start: 0.9227 (m) cc_final: 0.9020 (p) REVERT: A 408 MET cc_start: 0.7870 (mmm) cc_final: 0.7355 (mmm) REVERT: A 427 ASP cc_start: 0.8868 (m-30) cc_final: 0.8623 (m-30) REVERT: A 463 MET cc_start: 0.8748 (mtp) cc_final: 0.8416 (mmm) REVERT: A 511 LYS cc_start: 0.8767 (mttt) cc_final: 0.8453 (mmmt) REVERT: A 527 MET cc_start: 0.9433 (mtm) cc_final: 0.9096 (mtt) REVERT: A 531 PHE cc_start: 0.9486 (m-10) cc_final: 0.9133 (m-10) REVERT: A 624 LEU cc_start: 0.9283 (mt) cc_final: 0.9003 (tp) REVERT: A 670 MET cc_start: 0.8398 (mmm) cc_final: 0.8110 (mmm) REVERT: A 807 MET cc_start: 0.9384 (mmp) cc_final: 0.8829 (mtt) REVERT: B 126 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8694 (mt-10) REVERT: B 221 ILE cc_start: 0.9063 (mt) cc_final: 0.8849 (mm) REVERT: B 361 MET cc_start: 0.6908 (mmm) cc_final: 0.6360 (tpp) REVERT: B 521 LEU cc_start: 0.9210 (tt) cc_final: 0.8338 (tp) REVERT: B 526 TRP cc_start: 0.9409 (m100) cc_final: 0.8736 (m100) REVERT: B 670 MET cc_start: 0.9194 (mtp) cc_final: 0.8618 (mmt) REVERT: B 807 MET cc_start: 0.9648 (mmp) cc_final: 0.9408 (mmm) REVERT: C 85 ILE cc_start: 0.8875 (mm) cc_final: 0.8623 (tp) REVERT: C 267 GLU cc_start: 0.9203 (tt0) cc_final: 0.8881 (tm-30) REVERT: C 361 MET cc_start: 0.7945 (mmm) cc_final: 0.7594 (tpp) REVERT: C 408 MET cc_start: 0.7860 (mmp) cc_final: 0.7553 (mmm) REVERT: C 427 ASP cc_start: 0.8955 (m-30) cc_final: 0.8628 (m-30) REVERT: C 517 PHE cc_start: 0.8994 (t80) cc_final: 0.8552 (t80) REVERT: C 528 CYS cc_start: 0.9814 (m) cc_final: 0.8739 (m) REVERT: C 659 PHE cc_start: 0.9542 (m-80) cc_final: 0.9160 (m-80) REVERT: C 721 MET cc_start: 0.9355 (ptm) cc_final: 0.9082 (ppp) REVERT: C 723 VAL cc_start: 0.8801 (m) cc_final: 0.8302 (m) REVERT: D 126 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8681 (mt-10) REVERT: D 159 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 221 ILE cc_start: 0.8898 (mt) cc_final: 0.8663 (mm) REVERT: D 361 MET cc_start: 0.7534 (mmm) cc_final: 0.6677 (mmm) REVERT: D 424 TYR cc_start: 0.7739 (t80) cc_final: 0.6982 (t80) REVERT: D 521 LEU cc_start: 0.9125 (tt) cc_final: 0.8607 (tp) REVERT: D 526 TRP cc_start: 0.9416 (m100) cc_final: 0.9160 (m100) REVERT: D 617 THR cc_start: 0.9195 (m) cc_final: 0.8840 (p) REVERT: D 670 MET cc_start: 0.9143 (mtp) cc_final: 0.8437 (mmm) REVERT: D 710 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8874 (tt0) REVERT: D 807 MET cc_start: 0.9663 (mmp) cc_final: 0.9416 (mmm) REVERT: E 121 LYS cc_start: 0.9421 (mttt) cc_final: 0.9008 (tmtt) REVERT: E 146 CYS cc_start: 0.7210 (m) cc_final: 0.6680 (t) REVERT: E 220 MET cc_start: 0.9493 (mmp) cc_final: 0.9181 (mmm) REVERT: F 121 LYS cc_start: 0.9428 (mttt) cc_final: 0.8997 (tmtt) REVERT: F 146 CYS cc_start: 0.7404 (m) cc_final: 0.6869 (t) outliers start: 4 outliers final: 0 residues processed: 422 average time/residue: 0.1727 time to fit residues: 119.6601 Evaluate side-chains 290 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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: 9.9990 chunk 8 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 253 optimal weight: 0.8980 chunk 121 optimal weight: 0.0570 chunk 203 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN B 46 HIS B 65 GLN B 147 GLN B 246 GLN B 355 ASN B 619 ASN C 214 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 709 ASN C 756 GLN D 147 GLN D 246 GLN D 344 ASN D 412 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.035339 restraints weight = 204172.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.036561 restraints weight = 125791.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037401 restraints weight = 89205.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037997 restraints weight = 69515.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038395 restraints weight = 57885.732| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28172 Z= 0.144 Angle : 0.576 8.181 38108 Z= 0.307 Chirality : 0.040 0.198 4236 Planarity : 0.005 0.105 4768 Dihedral : 5.219 66.354 3794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.29 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % 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: 0.52 (0.15), residues: 3452 helix: 1.37 (0.13), residues: 1687 sheet: -1.82 (0.25), residues: 396 loop : -0.14 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 199 TYR 0.020 0.002 TYR B 450 PHE 0.025 0.002 PHE C 623 TRP 0.028 0.002 TRP E 198 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (28162) covalent geometry : angle 0.57475 / 0.31 (38088) SS BOND : bond 0.00308 / 0.16 ( 10) SS BOND : angle 2.02718 / 1.27 ( 20) hydrogen bonds : bond 0.03631 / 2.44 ( 1381) hydrogen bonds : angle 4.96910 / 3.47 ( 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 355 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 0.845 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: A 129 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8913 (pp30) REVERT: A 194 LEU cc_start: 0.9594 (tp) cc_final: 0.9167 (tp) REVERT: A 407 MET cc_start: 0.8310 (mtm) cc_final: 0.8049 (mpp) REVERT: A 408 MET cc_start: 0.8502 (mmm) cc_final: 0.8218 (mmm) REVERT: A 414 MET cc_start: 0.9153 (tpp) cc_final: 0.8905 (tpp) REVERT: A 427 ASP cc_start: 0.9085 (m-30) cc_final: 0.8706 (m-30) REVERT: A 463 MET cc_start: 0.9134 (mtp) cc_final: 0.8788 (mmm) REVERT: A 511 LYS cc_start: 0.8863 (mttt) cc_final: 0.8531 (mmmt) REVERT: A 670 MET cc_start: 0.8757 (mmm) cc_final: 0.8241 (mmm) REVERT: A 807 MET cc_start: 0.9457 (mmp) cc_final: 0.8845 (mtt) REVERT: B 361 MET cc_start: 0.7580 (mmm) cc_final: 0.7223 (tpp) REVERT: B 408 MET cc_start: 0.6972 (mmm) cc_final: 0.6164 (mmm) REVERT: B 517 PHE cc_start: 0.9186 (t80) cc_final: 0.8853 (t80) REVERT: B 521 LEU cc_start: 0.9128 (tt) cc_final: 0.8419 (tp) REVERT: B 526 TRP cc_start: 0.9452 (m100) cc_final: 0.8943 (m100) REVERT: C 194 LEU cc_start: 0.9700 (tp) cc_final: 0.9493 (tp) REVERT: C 267 GLU cc_start: 0.9184 (tt0) cc_final: 0.8922 (tm-30) REVERT: C 361 MET cc_start: 0.8254 (mmm) cc_final: 0.7725 (mmm) REVERT: C 427 ASP cc_start: 0.9146 (m-30) cc_final: 0.8744 (m-30) REVERT: C 496 MET cc_start: 0.8652 (mtp) cc_final: 0.8401 (mtm) REVERT: C 527 MET cc_start: 0.8986 (ppp) cc_final: 0.8683 (ppp) REVERT: C 528 CYS cc_start: 0.9619 (m) cc_final: 0.9171 (m) REVERT: C 608 PHE cc_start: 0.9088 (t80) cc_final: 0.8871 (t80) REVERT: C 659 PHE cc_start: 0.9621 (m-80) cc_final: 0.9289 (m-80) REVERT: C 670 MET cc_start: 0.8990 (mmt) cc_final: 0.8657 (mmp) REVERT: C 704 LEU cc_start: 0.8019 (tp) cc_final: 0.7763 (tp) REVERT: C 721 MET cc_start: 0.9427 (ptm) cc_final: 0.9021 (ptm) REVERT: D 93 HIS cc_start: 0.8516 (m90) cc_final: 0.8263 (m90) REVERT: D 159 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 221 ILE cc_start: 0.9202 (mt) cc_final: 0.8984 (mm) REVERT: D 380 MET cc_start: 0.8802 (mtp) cc_final: 0.8364 (mtp) REVERT: D 521 LEU cc_start: 0.9011 (tt) cc_final: 0.8353 (tp) REVERT: D 526 TRP cc_start: 0.9468 (m100) cc_final: 0.8959 (m100) REVERT: D 605 TRP cc_start: 0.9154 (t-100) cc_final: 0.8463 (t60) REVERT: D 710 GLU cc_start: 0.9526 (mt-10) cc_final: 0.8976 (tt0) REVERT: E 100 GLU cc_start: 0.8721 (tt0) cc_final: 0.8174 (tp30) REVERT: E 121 LYS cc_start: 0.9405 (mttt) cc_final: 0.8888 (tmtt) REVERT: E 146 CYS cc_start: 0.7316 (m) cc_final: 0.6918 (t) REVERT: E 182 MET cc_start: 0.9311 (mmp) cc_final: 0.9099 (mmm) REVERT: E 220 MET cc_start: 0.9553 (mmp) cc_final: 0.9274 (mmm) REVERT: F 100 GLU cc_start: 0.8699 (tt0) cc_final: 0.8181 (tp30) REVERT: F 121 LYS cc_start: 0.9460 (mttt) cc_final: 0.9048 (tmtt) REVERT: F 146 CYS cc_start: 0.7543 (m) cc_final: 0.7130 (t) outliers start: 3 outliers final: 1 residues processed: 354 average time/residue: 0.1685 time to fit residues: 97.8097 Evaluate side-chains 248 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 6.9990 chunk 279 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 197 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 355 ASN B 412 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS F 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.035604 restraints weight = 199755.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036834 restraints weight = 123764.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037684 restraints weight = 87993.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.038293 restraints weight = 68695.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038729 restraints weight = 57210.287| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28172 Z= 0.104 Angle : 0.524 8.758 38108 Z= 0.272 Chirality : 0.040 0.176 4236 Planarity : 0.004 0.067 4768 Dihedral : 4.950 65.406 3794 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.45 % Favored : 96.18 % Rotamer: Outliers : 0.07 % Allowed : 1.38 % Favored : 98.55 % 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: 1.62 (0.13), residues: 1689 sheet: -1.63 (0.25), residues: 420 loop : -0.17 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 675 TYR 0.018 0.001 TYR D 450 PHE 0.022 0.001 PHE C 623 TRP 0.021 0.001 TRP A 262 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (28162) covalent geometry : angle 0.52218 / 0.27 (38088) SS BOND : bond 0.00188 / 0.10 ( 10) SS BOND : angle 1.77697 / 1.11 ( 20) hydrogen bonds : bond 0.03167 / 2.13 ( 1381) hydrogen bonds : angle 4.65431 / 3.25 ( 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 328 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.011 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: A 129 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8906 (pp30) REVERT: A 194 LEU cc_start: 0.9650 (tp) cc_final: 0.9340 (tp) REVERT: A 407 MET cc_start: 0.8176 (mtm) cc_final: 0.7954 (mpp) REVERT: A 427 ASP cc_start: 0.9080 (m-30) cc_final: 0.8665 (m-30) REVERT: A 463 MET cc_start: 0.9096 (mtp) cc_final: 0.8749 (mmm) REVERT: A 511 LYS cc_start: 0.8863 (mttt) cc_final: 0.8502 (mmmt) REVERT: A 638 ASP cc_start: 0.9425 (m-30) cc_final: 0.9204 (m-30) REVERT: A 674 MET cc_start: 0.9222 (ttm) cc_final: 0.8489 (mmm) REVERT: A 721 MET cc_start: 0.9259 (ptm) cc_final: 0.9040 (ptm) REVERT: B 361 MET cc_start: 0.7948 (mmm) cc_final: 0.7613 (tpp) REVERT: B 408 MET cc_start: 0.7097 (mmm) cc_final: 0.6388 (mmm) REVERT: B 412 HIS cc_start: 0.8690 (p-80) cc_final: 0.8472 (p-80) REVERT: B 521 LEU cc_start: 0.9080 (tt) cc_final: 0.8496 (tt) REVERT: B 526 TRP cc_start: 0.9464 (m100) cc_final: 0.9122 (m100) REVERT: B 540 LEU cc_start: 0.9455 (mt) cc_final: 0.9211 (mp) REVERT: B 807 MET cc_start: 0.9645 (mmp) cc_final: 0.9397 (mmm) REVERT: C 14 ILE cc_start: 0.9584 (pt) cc_final: 0.9222 (mm) REVERT: C 88 PHE cc_start: 0.8750 (m-80) cc_final: 0.8492 (m-80) REVERT: C 361 MET cc_start: 0.8202 (mmm) cc_final: 0.7677 (mmm) REVERT: C 427 ASP cc_start: 0.9127 (m-30) cc_final: 0.8687 (m-30) REVERT: C 496 MET cc_start: 0.8603 (mtp) cc_final: 0.8319 (mtm) REVERT: C 608 PHE cc_start: 0.9120 (t80) cc_final: 0.8882 (t80) REVERT: C 659 PHE cc_start: 0.9561 (m-80) cc_final: 0.9292 (m-80) REVERT: C 670 MET cc_start: 0.9059 (mmt) cc_final: 0.8739 (mmm) REVERT: C 674 MET cc_start: 0.9480 (ptm) cc_final: 0.8956 (ppp) REVERT: C 704 LEU cc_start: 0.7674 (tp) cc_final: 0.7347 (tp) REVERT: D 93 HIS cc_start: 0.8525 (m90) cc_final: 0.8240 (m90) REVERT: D 159 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 221 ILE cc_start: 0.9241 (mt) cc_final: 0.9032 (mm) REVERT: D 361 MET cc_start: 0.8304 (mmp) cc_final: 0.7053 (tpp) REVERT: D 380 MET cc_start: 0.8843 (mtp) cc_final: 0.8269 (mtp) REVERT: D 521 LEU cc_start: 0.8980 (tt) cc_final: 0.8501 (tp) REVERT: D 526 TRP cc_start: 0.9447 (m100) cc_final: 0.9164 (m100) REVERT: D 605 TRP cc_start: 0.9249 (t-100) cc_final: 0.8670 (t60) REVERT: E 100 GLU cc_start: 0.8735 (tt0) cc_final: 0.8128 (tp30) REVERT: E 121 LYS cc_start: 0.9372 (mttt) cc_final: 0.8867 (tmtt) REVERT: E 146 CYS cc_start: 0.7394 (m) cc_final: 0.6920 (t) REVERT: E 182 MET cc_start: 0.9329 (mmp) cc_final: 0.9126 (mmp) REVERT: E 220 MET cc_start: 0.9588 (mmp) cc_final: 0.9346 (mmm) REVERT: F 21 PHE cc_start: 0.8785 (m-80) cc_final: 0.8566 (m-80) REVERT: F 100 GLU cc_start: 0.8702 (tt0) cc_final: 0.8160 (tp30) REVERT: F 121 LYS cc_start: 0.9459 (mttt) cc_final: 0.8981 (tmtt) REVERT: F 146 CYS cc_start: 0.7565 (m) cc_final: 0.7102 (t) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.1712 time to fit residues: 92.7135 Evaluate side-chains 235 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 8.9990 chunk 222 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 266 optimal weight: 0.0030 chunk 241 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS B 46 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** D 65 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN E 228 ASN F 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.046514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035098 restraints weight = 201598.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036303 restraints weight = 125401.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.037150 restraints weight = 89407.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.037759 restraints weight = 69860.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.038193 restraints weight = 58235.201| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28172 Z= 0.114 Angle : 0.518 8.414 38108 Z= 0.272 Chirality : 0.039 0.162 4236 Planarity : 0.004 0.062 4768 Dihedral : 4.861 63.783 3794 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.88 % Favored : 95.71 % Rotamer: Outliers : 0.03 % Allowed : 0.81 % Favored : 99.16 % 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: 1.75 (0.13), residues: 1691 sheet: -1.44 (0.25), residues: 418 loop : -0.14 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 675 TYR 0.013 0.001 TYR C 77 PHE 0.021 0.001 PHE A 29 TRP 0.029 0.001 TRP E 213 HIS 0.008 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (28162) covalent geometry : angle 0.51695 / 0.27 (38088) SS BOND : bond 0.00158 / 0.08 ( 10) SS BOND : angle 1.70743 / 1.07 ( 20) hydrogen bonds : bond 0.03093 / 2.08 ( 1381) hydrogen bonds : angle 4.51423 / 3.15 ( 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 303 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.932 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 194 LEU cc_start: 0.9637 (tp) cc_final: 0.9365 (tp) REVERT: A 408 MET cc_start: 0.7732 (tpt) cc_final: 0.7337 (tpt) REVERT: A 427 ASP cc_start: 0.9148 (m-30) cc_final: 0.8720 (m-30) REVERT: A 463 MET cc_start: 0.9204 (mtp) cc_final: 0.8857 (mmm) REVERT: A 496 MET cc_start: 0.9002 (mmp) cc_final: 0.8778 (mmm) REVERT: A 511 LYS cc_start: 0.8894 (mttt) cc_final: 0.8591 (mmmt) REVERT: A 526 TRP cc_start: 0.9246 (m100) cc_final: 0.8889 (m100) REVERT: A 674 MET cc_start: 0.9176 (ttm) cc_final: 0.8713 (mmm) REVERT: A 721 MET cc_start: 0.9291 (ptm) cc_final: 0.9035 (ptm) REVERT: B 25 GLU cc_start: 0.9027 (mp0) cc_final: 0.8588 (mm-30) REVERT: B 79 LYS cc_start: 0.9244 (pttp) cc_final: 0.8974 (pttt) REVERT: B 89 CYS cc_start: 0.8238 (m) cc_final: 0.7451 (p) REVERT: B 361 MET cc_start: 0.8330 (mmm) cc_final: 0.8017 (tpp) REVERT: B 408 MET cc_start: 0.7161 (mmm) cc_final: 0.6525 (mmm) REVERT: B 412 HIS cc_start: 0.8701 (p-80) cc_final: 0.8465 (p-80) REVERT: B 521 LEU cc_start: 0.9040 (tt) cc_final: 0.8247 (tp) REVERT: B 526 TRP cc_start: 0.9465 (m100) cc_final: 0.8883 (m100) REVERT: B 807 MET cc_start: 0.9594 (mmp) cc_final: 0.9382 (mmm) REVERT: C 88 PHE cc_start: 0.8916 (m-80) cc_final: 0.8653 (m-80) REVERT: C 194 LEU cc_start: 0.9671 (tp) cc_final: 0.9413 (tp) REVERT: C 361 MET cc_start: 0.8253 (mmm) cc_final: 0.7755 (mmm) REVERT: C 427 ASP cc_start: 0.9184 (m-30) cc_final: 0.8727 (m-30) REVERT: C 463 MET cc_start: 0.9492 (mmt) cc_final: 0.8977 (tpp) REVERT: C 521 LEU cc_start: 0.8512 (tp) cc_final: 0.8273 (tp) REVERT: C 527 MET cc_start: 0.9037 (ppp) cc_final: 0.8784 (ppp) REVERT: C 608 PHE cc_start: 0.9215 (t80) cc_final: 0.8928 (t80) REVERT: C 627 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8663 (mt-10) REVERT: C 659 PHE cc_start: 0.9571 (m-80) cc_final: 0.9364 (m-80) REVERT: C 670 MET cc_start: 0.9136 (mmt) cc_final: 0.8877 (mmm) REVERT: C 704 LEU cc_start: 0.7798 (tp) cc_final: 0.7476 (tp) REVERT: D 89 CYS cc_start: 0.8096 (m) cc_final: 0.7879 (m) REVERT: D 159 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 235 ILE cc_start: 0.9730 (pt) cc_final: 0.9340 (tp) REVERT: D 361 MET cc_start: 0.8335 (mmp) cc_final: 0.7812 (mmt) REVERT: D 380 MET cc_start: 0.8908 (mtp) cc_final: 0.8319 (mtp) REVERT: D 408 MET cc_start: 0.8098 (mmm) cc_final: 0.7519 (mmm) REVERT: D 412 HIS cc_start: 0.8412 (p90) cc_final: 0.8114 (p90) REVERT: D 521 LEU cc_start: 0.9017 (tt) cc_final: 0.8488 (tp) REVERT: D 526 TRP cc_start: 0.9470 (m100) cc_final: 0.9122 (m100) REVERT: D 605 TRP cc_start: 0.9293 (t-100) cc_final: 0.8714 (t60) REVERT: D 609 THR cc_start: 0.9522 (t) cc_final: 0.9236 (p) REVERT: E 100 GLU cc_start: 0.8730 (tt0) cc_final: 0.8102 (tp30) REVERT: E 121 LYS cc_start: 0.9405 (mttt) cc_final: 0.8877 (tmtt) REVERT: E 146 CYS cc_start: 0.7380 (m) cc_final: 0.6884 (t) REVERT: E 182 MET cc_start: 0.9340 (mmp) cc_final: 0.9125 (mmm) REVERT: E 220 MET cc_start: 0.9645 (mmp) cc_final: 0.9337 (mmm) REVERT: F 21 PHE cc_start: 0.8764 (m-80) cc_final: 0.8534 (m-80) REVERT: F 100 GLU cc_start: 0.8687 (tt0) cc_final: 0.8095 (tp30) REVERT: F 121 LYS cc_start: 0.9463 (mttt) cc_final: 0.9027 (tmtt) REVERT: F 146 CYS cc_start: 0.7674 (m) cc_final: 0.7240 (t) REVERT: F 181 MET cc_start: 0.9748 (mmm) cc_final: 0.9305 (mpp) REVERT: F 182 MET cc_start: 0.9173 (mmp) cc_final: 0.8959 (mmp) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1763 time to fit residues: 88.2398 Evaluate side-chains 225 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN A 311 ASN A 325 GLN A 337 GLN A 355 ASN A 791 ASN ** 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** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN F 15 ASN F 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.033431 restraints weight = 212810.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034554 restraints weight = 132965.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035348 restraints weight = 95780.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.035903 restraints weight = 75674.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.036261 restraints weight = 63789.877| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28172 Z= 0.193 Angle : 0.615 8.590 38108 Z= 0.327 Chirality : 0.041 0.206 4236 Planarity : 0.005 0.092 4768 Dihedral : 5.227 60.908 3794 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.41 % 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: 0.74 (0.15), residues: 3452 helix: 1.60 (0.13), residues: 1683 sheet: -1.53 (0.25), residues: 396 loop : -0.16 (0.18), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 303 TYR 0.023 0.002 TYR D 673 PHE 0.024 0.002 PHE B 659 TRP 0.027 0.002 TRP F 31 HIS 0.011 0.002 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (28162) covalent geometry : angle 0.61348 / 0.33 (38088) SS BOND : bond 0.00207 / 0.12 ( 10) SS BOND : angle 1.79698 / 1.13 ( 20) hydrogen bonds : bond 0.03723 / 2.51 ( 1381) hydrogen bonds : angle 4.78553 / 3.34 ( 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 256 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.210 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 463 MET cc_start: 0.9303 (mtp) cc_final: 0.8865 (mmm) REVERT: A 511 LYS cc_start: 0.8813 (mttt) cc_final: 0.8473 (mmmt) REVERT: A 526 TRP cc_start: 0.9292 (m100) cc_final: 0.8850 (m100) REVERT: A 638 ASP cc_start: 0.9502 (m-30) cc_final: 0.9300 (m-30) REVERT: A 674 MET cc_start: 0.9389 (ttm) cc_final: 0.8909 (mmm) REVERT: A 721 MET cc_start: 0.9271 (ptm) cc_final: 0.8993 (ptm) REVERT: B 79 LYS cc_start: 0.9416 (pttp) cc_final: 0.8802 (pttm) REVERT: B 89 CYS cc_start: 0.8885 (m) cc_final: 0.8173 (p) REVERT: B 235 ILE cc_start: 0.9823 (pt) cc_final: 0.9609 (mm) REVERT: B 408 MET cc_start: 0.7632 (mmm) cc_final: 0.6907 (mmm) REVERT: B 412 HIS cc_start: 0.8856 (p-80) cc_final: 0.8635 (p-80) REVERT: C 88 PHE cc_start: 0.9062 (m-80) cc_final: 0.8804 (m-80) REVERT: C 113 MET cc_start: 0.9476 (mmp) cc_final: 0.9194 (mmp) REVERT: C 361 MET cc_start: 0.8544 (mmm) cc_final: 0.8299 (mmm) REVERT: C 408 MET cc_start: 0.8642 (mmp) cc_final: 0.8099 (mmp) REVERT: C 424 TYR cc_start: 0.9359 (t80) cc_final: 0.9117 (t80) REVERT: C 427 ASP cc_start: 0.9331 (m-30) cc_final: 0.8912 (m-30) REVERT: C 527 MET cc_start: 0.9087 (ppp) cc_final: 0.8815 (ppp) REVERT: C 608 PHE cc_start: 0.9354 (t80) cc_final: 0.9023 (t80) REVERT: C 659 PHE cc_start: 0.9623 (m-80) cc_final: 0.9377 (m-80) REVERT: C 721 MET cc_start: 0.9229 (ptm) cc_final: 0.8946 (ptm) REVERT: C 807 MET cc_start: 0.9108 (mtt) cc_final: 0.8780 (mmp) REVERT: D 159 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 235 ILE cc_start: 0.9850 (pt) cc_final: 0.9613 (tp) REVERT: D 361 MET cc_start: 0.8885 (mmp) cc_final: 0.8304 (mmt) REVERT: D 384 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8884 (tp30) REVERT: D 408 MET cc_start: 0.8301 (mmm) cc_final: 0.7770 (mmm) REVERT: D 412 HIS cc_start: 0.8560 (p90) cc_final: 0.8222 (p90) REVERT: D 605 TRP cc_start: 0.9436 (t-100) cc_final: 0.9037 (t60) REVERT: D 609 THR cc_start: 0.9579 (t) cc_final: 0.9283 (p) REVERT: D 659 PHE cc_start: 0.9244 (m-80) cc_final: 0.8901 (m-80) REVERT: E 100 GLU cc_start: 0.8706 (tt0) cc_final: 0.7951 (tp30) REVERT: E 121 LYS cc_start: 0.9444 (mttt) cc_final: 0.8882 (tmtt) REVERT: E 146 CYS cc_start: 0.7575 (m) cc_final: 0.7033 (t) REVERT: E 182 MET cc_start: 0.9378 (mmp) cc_final: 0.9162 (mmm) REVERT: E 220 MET cc_start: 0.9637 (mmp) cc_final: 0.9249 (mmm) REVERT: F 100 GLU cc_start: 0.8655 (tt0) cc_final: 0.8012 (tp30) REVERT: F 121 LYS cc_start: 0.9447 (mttt) cc_final: 0.8992 (tmtt) REVERT: F 146 CYS cc_start: 0.7767 (m) cc_final: 0.7327 (t) outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.1685 time to fit residues: 72.3153 Evaluate side-chains 194 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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: 9.9990 chunk 176 optimal weight: 0.0570 chunk 108 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 249 optimal weight: 0.4980 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** 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** D 65 GLN ** D 412 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 = 0.3016 r_free = 0.3016 target = 0.044512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033409 restraints weight = 210482.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.034536 restraints weight = 131725.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035323 restraints weight = 94711.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.035885 restraints weight = 74809.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.036235 restraints weight = 63030.752| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28172 Z= 0.161 Angle : 0.565 10.125 38108 Z= 0.299 Chirality : 0.040 0.265 4236 Planarity : 0.004 0.071 4768 Dihedral : 5.042 56.480 3794 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.82 (0.15), residues: 3452 helix: 1.70 (0.13), residues: 1703 sheet: -1.34 (0.25), residues: 396 loop : -0.26 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.016 0.001 TYR C 77 PHE 0.027 0.002 PHE A 541 TRP 0.019 0.001 TRP D 606 HIS 0.010 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (28162) covalent geometry : angle 0.56321 / 0.30 (38088) SS BOND : bond 0.00243 / 0.13 ( 10) SS BOND : angle 1.88159 / 1.14 ( 20) hydrogen bonds : bond 0.03364 / 2.27 ( 1381) hydrogen bonds : angle 4.60111 / 3.21 ( 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 245 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.8959 (m-80) cc_final: 0.8623 (m-80) REVERT: A 89 CYS cc_start: 0.8581 (m) cc_final: 0.7925 (p) REVERT: A 113 MET cc_start: 0.9493 (mmp) cc_final: 0.9267 (mmp) REVERT: A 408 MET cc_start: 0.8184 (tpt) cc_final: 0.7859 (tpp) REVERT: A 463 MET cc_start: 0.9404 (mtp) cc_final: 0.9054 (mmt) REVERT: A 496 MET cc_start: 0.8903 (mmm) cc_final: 0.8663 (mmm) REVERT: A 511 LYS cc_start: 0.8841 (mttt) cc_final: 0.8524 (mmmt) REVERT: A 674 MET cc_start: 0.9357 (ttm) cc_final: 0.9039 (mmm) REVERT: A 721 MET cc_start: 0.9287 (ptm) cc_final: 0.9006 (ptm) REVERT: B 25 GLU cc_start: 0.9192 (mp0) cc_final: 0.8680 (mm-30) REVERT: B 33 MET cc_start: 0.9169 (ppp) cc_final: 0.8858 (ptt) REVERT: B 79 LYS cc_start: 0.9447 (pttp) cc_final: 0.9098 (pttt) REVERT: B 89 CYS cc_start: 0.9054 (m) cc_final: 0.8293 (p) REVERT: B 292 MET cc_start: 0.9271 (ptp) cc_final: 0.9028 (ptt) REVERT: B 407 MET cc_start: 0.9040 (mmp) cc_final: 0.8748 (mmm) REVERT: B 408 MET cc_start: 0.7683 (mmm) cc_final: 0.6883 (mmm) REVERT: B 412 HIS cc_start: 0.8885 (p-80) cc_final: 0.8671 (p-80) REVERT: B 605 TRP cc_start: 0.9219 (t-100) cc_final: 0.8888 (t-100) REVERT: B 659 PHE cc_start: 0.9281 (m-80) cc_final: 0.9035 (m-80) REVERT: B 670 MET cc_start: 0.9530 (ptt) cc_final: 0.9053 (ppp) REVERT: B 807 MET cc_start: 0.9647 (mmp) cc_final: 0.9347 (mmm) REVERT: C 88 PHE cc_start: 0.9115 (m-80) cc_final: 0.8883 (m-80) REVERT: C 89 CYS cc_start: 0.8762 (m) cc_final: 0.7987 (p) REVERT: C 113 MET cc_start: 0.9463 (mmp) cc_final: 0.9174 (mmp) REVERT: C 361 MET cc_start: 0.8554 (mmm) cc_final: 0.8353 (mmm) REVERT: C 407 MET cc_start: 0.7939 (pmm) cc_final: 0.7728 (pmm) REVERT: C 408 MET cc_start: 0.8803 (mmp) cc_final: 0.8326 (mmm) REVERT: C 463 MET cc_start: 0.9604 (mmt) cc_final: 0.9372 (mmm) REVERT: C 527 MET cc_start: 0.9053 (ppp) cc_final: 0.8824 (ppp) REVERT: C 608 PHE cc_start: 0.9359 (t80) cc_final: 0.9026 (t80) REVERT: C 659 PHE cc_start: 0.9638 (m-80) cc_final: 0.9409 (m-80) REVERT: C 670 MET cc_start: 0.9499 (mmp) cc_final: 0.9118 (mmm) REVERT: C 674 MET cc_start: 0.9559 (ptm) cc_final: 0.8881 (ppp) REVERT: C 704 LEU cc_start: 0.8851 (tp) cc_final: 0.8492 (tt) REVERT: C 708 MET cc_start: 0.9060 (mmp) cc_final: 0.8835 (mmm) REVERT: C 721 MET cc_start: 0.9246 (ptm) cc_final: 0.9031 (ptm) REVERT: C 807 MET cc_start: 0.8988 (mtt) cc_final: 0.8738 (mmp) REVERT: D 25 GLU cc_start: 0.9102 (mp0) cc_final: 0.8639 (mm-30) REVERT: D 33 MET cc_start: 0.9025 (ptt) cc_final: 0.8760 (ptt) REVERT: D 159 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 361 MET cc_start: 0.8692 (mmp) cc_final: 0.8212 (mmp) REVERT: D 384 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8878 (tp30) REVERT: D 408 MET cc_start: 0.8364 (mmm) cc_final: 0.7722 (mmm) REVERT: D 412 HIS cc_start: 0.8543 (p90) cc_final: 0.8159 (p90) REVERT: D 496 MET cc_start: 0.8806 (ppp) cc_final: 0.8547 (ppp) REVERT: D 605 TRP cc_start: 0.9402 (t-100) cc_final: 0.8903 (t60) REVERT: D 609 THR cc_start: 0.9520 (t) cc_final: 0.9275 (p) REVERT: D 633 ILE cc_start: 0.9276 (pt) cc_final: 0.9061 (mp) REVERT: D 659 PHE cc_start: 0.9308 (m-80) cc_final: 0.8737 (m-80) REVERT: D 708 MET cc_start: 0.9418 (mmp) cc_final: 0.9216 (mmm) REVERT: E 100 GLU cc_start: 0.8730 (tt0) cc_final: 0.7994 (tp30) REVERT: E 121 LYS cc_start: 0.9370 (mttt) cc_final: 0.8794 (tmtt) REVERT: E 146 CYS cc_start: 0.7499 (m) cc_final: 0.7072 (t) REVERT: E 182 MET cc_start: 0.9374 (mmp) cc_final: 0.9160 (mmm) REVERT: E 220 MET cc_start: 0.9609 (mmp) cc_final: 0.9263 (mmm) REVERT: F 100 GLU cc_start: 0.8689 (tt0) cc_final: 0.7994 (tp30) REVERT: F 121 LYS cc_start: 0.9439 (mttt) cc_final: 0.8948 (tmtt) REVERT: F 146 CYS cc_start: 0.7637 (m) cc_final: 0.7148 (t) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1606 time to fit residues: 66.0933 Evaluate side-chains 191 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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: 4.9990 chunk 286 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN C 236 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 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 = 0.3042 r_free = 0.3042 target = 0.045324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.033971 restraints weight = 206908.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035165 restraints weight = 127006.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036003 restraints weight = 90266.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036558 restraints weight = 70663.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036997 restraints weight = 59482.224| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28172 Z= 0.112 Angle : 0.538 9.849 38108 Z= 0.280 Chirality : 0.040 0.227 4236 Planarity : 0.004 0.068 4768 Dihedral : 4.882 57.752 3794 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.11 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.96 (0.15), residues: 3452 helix: 1.86 (0.13), residues: 1706 sheet: -1.15 (0.26), residues: 376 loop : -0.32 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 198 TYR 0.011 0.001 TYR B 711 PHE 0.029 0.001 PHE F 209 TRP 0.020 0.001 TRP A 262 HIS 0.008 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (28162) covalent geometry : angle 0.53670 / 0.28 (38088) SS BOND : bond 0.00228 / 0.13 ( 10) SS BOND : angle 1.82340 / 1.11 ( 20) hydrogen bonds : bond 0.03183 / 2.13 ( 1381) hydrogen bonds : angle 4.43490 / 3.11 ( 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 245 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9083 (m-80) cc_final: 0.8796 (m-80) REVERT: A 89 CYS cc_start: 0.8806 (m) cc_final: 0.8026 (p) REVERT: A 113 MET cc_start: 0.9510 (mmp) cc_final: 0.9240 (mmp) REVERT: A 408 MET cc_start: 0.8279 (tpt) cc_final: 0.7997 (tpp) REVERT: A 463 MET cc_start: 0.9427 (mtp) cc_final: 0.9089 (mmt) REVERT: A 518 LEU cc_start: 0.8858 (mt) cc_final: 0.8637 (mt) REVERT: A 526 TRP cc_start: 0.9307 (m100) cc_final: 0.8923 (m100) REVERT: A 527 MET cc_start: 0.9455 (mtm) cc_final: 0.9137 (ptp) REVERT: A 674 MET cc_start: 0.9348 (ttm) cc_final: 0.9072 (mmm) REVERT: A 721 MET cc_start: 0.9272 (ptm) cc_final: 0.8990 (ptt) REVERT: B 25 GLU cc_start: 0.9220 (mp0) cc_final: 0.8678 (mm-30) REVERT: B 79 LYS cc_start: 0.9360 (pttp) cc_final: 0.8985 (pttt) REVERT: B 89 CYS cc_start: 0.9100 (m) cc_final: 0.8358 (p) REVERT: B 235 ILE cc_start: 0.9823 (pt) cc_final: 0.9603 (mm) REVERT: B 361 MET cc_start: 0.8999 (mmm) cc_final: 0.8560 (tpp) REVERT: B 407 MET cc_start: 0.9185 (mmp) cc_final: 0.8956 (mmm) REVERT: B 408 MET cc_start: 0.7620 (mmm) cc_final: 0.6828 (mmm) REVERT: B 412 HIS cc_start: 0.8921 (p-80) cc_final: 0.8699 (p-80) REVERT: B 605 TRP cc_start: 0.9214 (t-100) cc_final: 0.8854 (t-100) REVERT: B 659 PHE cc_start: 0.9294 (m-80) cc_final: 0.9080 (m-80) REVERT: B 670 MET cc_start: 0.9609 (ptt) cc_final: 0.8937 (ppp) REVERT: C 88 PHE cc_start: 0.9215 (m-80) cc_final: 0.8985 (m-80) REVERT: C 89 CYS cc_start: 0.8827 (m) cc_final: 0.8057 (p) REVERT: C 113 MET cc_start: 0.9456 (mmp) cc_final: 0.9131 (mmp) REVERT: C 407 MET cc_start: 0.8066 (pmm) cc_final: 0.7849 (pmm) REVERT: C 408 MET cc_start: 0.8823 (mmp) cc_final: 0.8308 (mmm) REVERT: C 424 TYR cc_start: 0.9558 (t80) cc_final: 0.9271 (t80) REVERT: C 463 MET cc_start: 0.9626 (mmt) cc_final: 0.9422 (mmm) REVERT: C 521 LEU cc_start: 0.8373 (tp) cc_final: 0.7985 (tp) REVERT: C 527 MET cc_start: 0.9073 (ppp) cc_final: 0.8844 (ppp) REVERT: C 585 MET cc_start: 0.5406 (mtt) cc_final: 0.4484 (mtt) REVERT: C 608 PHE cc_start: 0.9379 (t80) cc_final: 0.9012 (t80) REVERT: C 659 PHE cc_start: 0.9654 (m-80) cc_final: 0.9453 (m-80) REVERT: C 670 MET cc_start: 0.9466 (mmp) cc_final: 0.9096 (mmm) REVERT: C 674 MET cc_start: 0.9465 (ptm) cc_final: 0.8940 (ppp) REVERT: C 704 LEU cc_start: 0.8691 (tp) cc_final: 0.8394 (tp) REVERT: C 708 MET cc_start: 0.9067 (mmp) cc_final: 0.8768 (mmm) REVERT: C 721 MET cc_start: 0.9261 (ptm) cc_final: 0.9026 (ptm) REVERT: C 807 MET cc_start: 0.8913 (mtt) cc_final: 0.8670 (mmp) REVERT: D 25 GLU cc_start: 0.9133 (mp0) cc_final: 0.8721 (mm-30) REVERT: D 33 MET cc_start: 0.8989 (ptt) cc_final: 0.8617 (ptt) REVERT: D 159 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8124 (tm-30) REVERT: D 361 MET cc_start: 0.8768 (mmp) cc_final: 0.8151 (mmm) REVERT: D 384 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8884 (tp30) REVERT: D 496 MET cc_start: 0.8730 (ppp) cc_final: 0.8484 (ppp) REVERT: D 609 THR cc_start: 0.9576 (t) cc_final: 0.9356 (p) REVERT: D 633 ILE cc_start: 0.9269 (pt) cc_final: 0.9066 (mp) REVERT: D 659 PHE cc_start: 0.9323 (m-80) cc_final: 0.8785 (m-80) REVERT: D 708 MET cc_start: 0.9312 (mmp) cc_final: 0.9086 (mmm) REVERT: E 100 GLU cc_start: 0.8722 (tt0) cc_final: 0.8005 (tp30) REVERT: E 121 LYS cc_start: 0.9326 (mttt) cc_final: 0.8736 (tmtt) REVERT: E 146 CYS cc_start: 0.7428 (m) cc_final: 0.6780 (t) REVERT: E 220 MET cc_start: 0.9586 (mmp) cc_final: 0.9251 (mmm) REVERT: F 100 GLU cc_start: 0.8686 (tt0) cc_final: 0.7995 (tp30) REVERT: F 121 LYS cc_start: 0.9508 (mttt) cc_final: 0.9073 (tmtt) REVERT: F 146 CYS cc_start: 0.7511 (m) cc_final: 0.6887 (t) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1622 time to fit residues: 66.9342 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 : 1.049 ------------------------------------------------------------------------------- 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: 0.9980 chunk 249 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 246 GLN ** 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** D 112 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.031797 restraints weight = 217152.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032926 restraints weight = 133918.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033707 restraints weight = 95453.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034222 restraints weight = 75127.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.034626 restraints weight = 63637.739| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28172 Z= 0.264 Angle : 0.681 10.176 38108 Z= 0.361 Chirality : 0.042 0.215 4236 Planarity : 0.005 0.076 4768 Dihedral : 5.423 58.137 3794 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.81 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.55 (0.15), residues: 3452 helix: 1.43 (0.13), residues: 1684 sheet: -1.22 (0.26), residues: 382 loop : -0.40 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG C 198 TYR 0.020 0.002 TYR B 421 PHE 0.024 0.002 PHE B 74 TRP 0.016 0.002 TRP E 198 HIS 0.011 0.002 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (28162) covalent geometry : angle 0.67920 / 0.36 (38088) SS BOND : bond 0.00334 / 0.18 ( 10) SS BOND : angle 2.18671 / 1.33 ( 20) hydrogen bonds : bond 0.03869 / 2.60 ( 1381) hydrogen bonds : angle 4.90179 / 3.44 ( 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 220 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9171 (m-80) cc_final: 0.8863 (m-80) REVERT: A 89 CYS cc_start: 0.8911 (m) cc_final: 0.8135 (p) REVERT: A 113 MET cc_start: 0.9622 (mmp) cc_final: 0.9167 (mmp) REVERT: A 463 MET cc_start: 0.9456 (mtp) cc_final: 0.9032 (mmt) REVERT: A 511 LYS cc_start: 0.8859 (mttt) cc_final: 0.8572 (mmmt) REVERT: A 527 MET cc_start: 0.9467 (mtm) cc_final: 0.9197 (mtt) REVERT: A 528 CYS cc_start: 0.9673 (m) cc_final: 0.9203 (t) REVERT: A 674 MET cc_start: 0.9428 (ttm) cc_final: 0.9106 (mmm) REVERT: A 721 MET cc_start: 0.9330 (ptm) cc_final: 0.9075 (ptm) REVERT: B 33 MET cc_start: 0.9216 (ppp) cc_final: 0.8884 (ptt) REVERT: B 79 LYS cc_start: 0.9492 (pttp) cc_final: 0.9104 (pttm) REVERT: B 89 CYS cc_start: 0.9127 (m) cc_final: 0.8560 (p) REVERT: B 93 HIS cc_start: 0.8873 (m90) cc_final: 0.8618 (m90) REVERT: B 361 MET cc_start: 0.9043 (mmm) cc_final: 0.8310 (tpp) REVERT: B 408 MET cc_start: 0.7918 (mmm) cc_final: 0.7689 (mmm) REVERT: B 670 MET cc_start: 0.9663 (ptt) cc_final: 0.9344 (ptp) REVERT: C 88 PHE cc_start: 0.9271 (m-80) cc_final: 0.9007 (m-80) REVERT: C 89 CYS cc_start: 0.8934 (m) cc_final: 0.8479 (p) REVERT: C 113 MET cc_start: 0.9551 (mmp) cc_final: 0.8988 (mmp) REVERT: C 407 MET cc_start: 0.8326 (pmm) cc_final: 0.7892 (pmm) REVERT: C 408 MET cc_start: 0.8824 (mmp) cc_final: 0.8573 (mmm) REVERT: C 527 MET cc_start: 0.9060 (ppp) cc_final: 0.8834 (ppp) REVERT: C 670 MET cc_start: 0.9486 (mmp) cc_final: 0.9177 (mmm) REVERT: C 674 MET cc_start: 0.9574 (ptm) cc_final: 0.8949 (ppp) REVERT: C 704 LEU cc_start: 0.9081 (tp) cc_final: 0.8807 (tp) REVERT: C 708 MET cc_start: 0.9189 (mmp) cc_final: 0.8905 (mmm) REVERT: C 807 MET cc_start: 0.8970 (mtt) cc_final: 0.8734 (mmp) REVERT: D 25 GLU cc_start: 0.9178 (mp0) cc_final: 0.8885 (mp0) REVERT: D 33 MET cc_start: 0.9058 (ptt) cc_final: 0.8656 (ptt) REVERT: D 361 MET cc_start: 0.8718 (mmp) cc_final: 0.8445 (mmp) REVERT: D 380 MET cc_start: 0.8763 (mtp) cc_final: 0.8372 (mtp) REVERT: D 384 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8926 (tp30) REVERT: D 605 TRP cc_start: 0.9434 (t-100) cc_final: 0.9055 (t60) REVERT: D 609 THR cc_start: 0.9533 (t) cc_final: 0.9313 (p) REVERT: D 659 PHE cc_start: 0.9370 (m-80) cc_final: 0.8879 (m-80) REVERT: E 100 GLU cc_start: 0.8679 (tt0) cc_final: 0.7902 (tp30) REVERT: E 121 LYS cc_start: 0.9180 (mttt) cc_final: 0.8522 (tmtt) REVERT: E 145 MET cc_start: 0.7365 (pmm) cc_final: 0.7154 (pmm) REVERT: E 146 CYS cc_start: 0.7638 (m) cc_final: 0.6940 (t) REVERT: E 182 MET cc_start: 0.9267 (mmp) cc_final: 0.9039 (mmm) REVERT: E 218 CYS cc_start: 0.8577 (m) cc_final: 0.7929 (t) REVERT: E 220 MET cc_start: 0.9586 (mmp) cc_final: 0.9223 (mmm) REVERT: F 100 GLU cc_start: 0.8696 (tt0) cc_final: 0.7958 (tp30) REVERT: F 121 LYS cc_start: 0.9435 (mttt) cc_final: 0.9008 (tmtt) REVERT: F 145 MET cc_start: 0.7517 (pmm) cc_final: 0.7282 (pmm) REVERT: F 146 CYS cc_start: 0.7626 (m) cc_final: 0.7036 (t) REVERT: F 181 MET cc_start: 0.9743 (mmm) cc_final: 0.9400 (mmm) REVERT: F 216 PHE cc_start: 0.9256 (t80) cc_final: 0.9043 (t80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1640 time to fit residues: 60.9522 Evaluate side-chains 171 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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: 0.9980 chunk 217 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 296 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 165 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 112 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 = 0.3032 r_free = 0.3032 target = 0.044965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033733 restraints weight = 207182.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034932 restraints weight = 126255.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035767 restraints weight = 89379.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.036350 restraints weight = 69877.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036775 restraints weight = 58423.422| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.9120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28172 Z= 0.107 Angle : 0.566 9.729 38108 Z= 0.290 Chirality : 0.040 0.228 4236 Planarity : 0.004 0.072 4768 Dihedral : 5.031 59.712 3794 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.00 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.84 (0.15), residues: 3452 helix: 1.72 (0.13), residues: 1707 sheet: -1.03 (0.28), residues: 338 loop : -0.43 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 198 TYR 0.011 0.001 TYR B 711 PHE 0.029 0.001 PHE F 21 TRP 0.021 0.001 TRP A 262 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (28162) covalent geometry : angle 0.56486 / 0.29 (38088) SS BOND : bond 0.00190 / 0.11 ( 10) SS BOND : angle 1.77397 / 1.07 ( 20) hydrogen bonds : bond 0.03218 / 2.15 ( 1381) hydrogen bonds : angle 4.41121 / 3.09 ( 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 235 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 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: A 89 CYS cc_start: 0.8867 (m) cc_final: 0.8038 (p) REVERT: A 113 MET cc_start: 0.9546 (mmp) cc_final: 0.9129 (mmp) REVERT: A 442 LEU cc_start: 0.9341 (mt) cc_final: 0.9123 (mt) REVERT: A 463 MET cc_start: 0.9465 (mtp) cc_final: 0.9145 (mmm) REVERT: A 521 LEU cc_start: 0.8453 (tp) cc_final: 0.7520 (tp) REVERT: A 526 TRP cc_start: 0.9325 (m100) cc_final: 0.8871 (m100) REVERT: A 721 MET cc_start: 0.9304 (ptm) cc_final: 0.9033 (ptt) REVERT: B 25 GLU cc_start: 0.9226 (mp0) cc_final: 0.8887 (mp0) REVERT: B 79 LYS cc_start: 0.9347 (pttp) cc_final: 0.8998 (pttt) REVERT: B 89 CYS cc_start: 0.9127 (m) cc_final: 0.8583 (p) REVERT: B 93 HIS cc_start: 0.8721 (m90) cc_final: 0.8487 (m90) REVERT: B 361 MET cc_start: 0.9097 (mmm) cc_final: 0.8640 (tpp) REVERT: B 407 MET cc_start: 0.9093 (mmp) cc_final: 0.8815 (mmm) REVERT: B 496 MET cc_start: 0.9060 (ppp) cc_final: 0.8785 (ppp) REVERT: B 605 TRP cc_start: 0.9325 (t-100) cc_final: 0.8871 (t60) REVERT: B 670 MET cc_start: 0.9697 (ptt) cc_final: 0.9052 (ppp) REVERT: C 89 CYS cc_start: 0.8918 (m) cc_final: 0.8312 (p) REVERT: C 113 MET cc_start: 0.9436 (mmp) cc_final: 0.9022 (mmp) REVERT: C 407 MET cc_start: 0.8231 (pmm) cc_final: 0.8025 (pmm) REVERT: C 408 MET cc_start: 0.9028 (mmp) cc_final: 0.8644 (mmm) REVERT: C 424 TYR cc_start: 0.9543 (t80) cc_final: 0.9317 (t80) REVERT: C 521 LEU cc_start: 0.8224 (tp) cc_final: 0.7836 (tp) REVERT: C 527 MET cc_start: 0.9014 (ppp) cc_final: 0.8768 (ppp) REVERT: C 670 MET cc_start: 0.9412 (mmp) cc_final: 0.9183 (mmm) REVERT: C 674 MET cc_start: 0.9472 (ptm) cc_final: 0.8951 (ppp) REVERT: C 704 LEU cc_start: 0.8895 (tp) cc_final: 0.8622 (tp) REVERT: C 708 MET cc_start: 0.9096 (mmp) cc_final: 0.8829 (mmm) REVERT: D 25 GLU cc_start: 0.9113 (mp0) cc_final: 0.8863 (mp0) REVERT: D 33 MET cc_start: 0.8952 (ptt) cc_final: 0.8573 (ptt) REVERT: D 104 ASP cc_start: 0.9206 (p0) cc_final: 0.9005 (p0) REVERT: D 110 VAL cc_start: 0.9050 (t) cc_final: 0.8777 (m) REVERT: D 159 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 361 MET cc_start: 0.8772 (mmp) cc_final: 0.8223 (mmm) REVERT: D 384 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8921 (tp30) REVERT: D 408 MET cc_start: 0.8504 (mmm) cc_final: 0.8127 (mmm) REVERT: D 412 HIS cc_start: 0.8609 (p-80) cc_final: 0.8403 (p-80) REVERT: D 586 GLN cc_start: 0.6925 (pt0) cc_final: 0.6721 (tm-30) REVERT: D 609 THR cc_start: 0.9514 (t) cc_final: 0.9301 (p) REVERT: D 659 PHE cc_start: 0.9345 (m-80) cc_final: 0.8800 (m-80) REVERT: E 100 GLU cc_start: 0.8678 (tt0) cc_final: 0.7944 (tp30) REVERT: E 121 LYS cc_start: 0.9268 (mttt) cc_final: 0.8558 (tmtt) REVERT: E 146 CYS cc_start: 0.7536 (m) cc_final: 0.6847 (t) REVERT: E 182 MET cc_start: 0.9081 (mmp) cc_final: 0.8853 (mmm) REVERT: E 218 CYS cc_start: 0.8585 (m) cc_final: 0.8044 (t) REVERT: E 220 MET cc_start: 0.9582 (mmp) cc_final: 0.9266 (mmm) REVERT: F 100 GLU cc_start: 0.8679 (tt0) cc_final: 0.7987 (tp30) REVERT: F 121 LYS cc_start: 0.9456 (mttt) cc_final: 0.9018 (tmtt) REVERT: F 146 CYS cc_start: 0.7519 (m) cc_final: 0.6890 (t) REVERT: F 181 MET cc_start: 0.9701 (mmm) cc_final: 0.9398 (mpp) REVERT: F 216 PHE cc_start: 0.9201 (t80) cc_final: 0.8981 (t80) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1649 time to fit residues: 65.4318 Evaluate side-chains 190 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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: 7.9990 chunk 138 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.032941 restraints weight = 210756.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034111 restraints weight = 129911.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.034929 restraints weight = 92502.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.035494 restraints weight = 72509.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.035899 restraints weight = 60936.525| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.9401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28172 Z= 0.151 Angle : 0.577 15.866 38108 Z= 0.299 Chirality : 0.040 0.224 4236 Planarity : 0.004 0.074 4768 Dihedral : 5.070 59.078 3794 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.26 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.87 (0.15), residues: 3452 helix: 1.77 (0.13), residues: 1703 sheet: -1.10 (0.27), residues: 360 loop : -0.40 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 198 TYR 0.014 0.001 TYR B 711 PHE 0.034 0.002 PHE A 584 TRP 0.017 0.001 TRP A 262 HIS 0.011 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (28162) covalent geometry : angle 0.57533 / 0.30 (38088) SS BOND : bond 0.00208 / 0.12 ( 10) SS BOND : angle 1.88498 / 1.14 ( 20) hydrogen bonds : bond 0.03271 / 2.19 ( 1381) hydrogen bonds : angle 4.47798 / 3.14 ( 3987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.35 seconds wall clock time: 71 minutes 52.17 seconds (4312.17 seconds total)