Starting phenix.real_space_refine on Mon Jul 6 01:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ss2_40741/07_2026/8ss2_40741.cif" } resolution = 3.58 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= 0.002 sd= 0.025 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 20 5.49 5 S 166 5.16 5 C 20273 2.51 5 N 4965 2.21 5 O 5710 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 66 residue(s): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31146 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "C" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 313 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 303 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.00, per 1000 atoms: 0.19 Number of scatterers: 31146 At special positions: 0 Unit cell: (117.03, 163.51, 197.54, 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 166 16.00 P 20 15.00 F 12 9.00 O 5710 8.00 N 4965 7.00 C 20273 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=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.00 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.06 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 38 sheets defined 46.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.562A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.582A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.788A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.082A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.926A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.736A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.617A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.511A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.625A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 300 removed outlier: 3.528A pdb=" N ASP A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.595A pdb=" N ASN A 311 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.529A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.659A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.881A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 3.642A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 removed outlier: 4.673A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.586A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.973A pdb=" N LYS A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.567A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.893A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 removed outlier: 3.739A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.798A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 817 removed outlier: 3.534A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.788A pdb=" N THR A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 4.280A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 986 removed outlier: 3.823A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1032 removed outlier: 3.781A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 4.324A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.512A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.929A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.085A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.817A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.153A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.569A pdb=" N SER B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.561A pdb=" N THR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 removed outlier: 4.156A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.513A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.731A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.512A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.838A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 546 removed outlier: 3.707A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.574A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.633A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 4.304A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.604A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 691 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.653A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.657A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 4.051A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.562A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.582A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 4.082A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.926A pdb=" N TYR C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.735A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.618A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.511A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.625A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.528A pdb=" N ASP C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.595A pdb=" N ASN C 311 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 423 through 436 removed outlier: 3.530A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.660A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.881A pdb=" N MET C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 615 removed outlier: 3.642A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 4.674A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.586A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.973A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.567A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.893A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 748 removed outlier: 3.739A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.799A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 817 removed outlier: 3.534A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.788A pdb=" N THR C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 4.281A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 986 removed outlier: 3.823A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1032 removed outlier: 3.781A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C1021 " --> pdb=" O THR C1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C1029 " --> pdb=" O VAL C1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 4.323A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.511A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 92 removed outlier: 3.929A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.086A pdb=" N LEU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.818A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 226 through 230 removed outlier: 4.154A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.569A pdb=" N SER D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 300 removed outlier: 3.562A pdb=" N THR D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 4.156A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.513A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.731A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.513A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.839A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 546 removed outlier: 3.707A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.575A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.633A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.304A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 677 removed outlier: 3.603A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 691 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.652A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.657A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 4.051A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 removed outlier: 3.661A pdb=" N MET E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 36 removed outlier: 3.539A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.529A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 85 removed outlier: 3.733A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 105 Proline residue: E 96 - end of helix removed outlier: 3.655A pdb=" N TYR E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 158 removed outlier: 3.811A pdb=" N GLU E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 150 " --> pdb=" O PHE E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 18 removed outlier: 3.661A pdb=" N MET F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 36 removed outlier: 3.540A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.529A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 85 removed outlier: 3.734A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 105 Proline residue: F 96 - end of helix removed outlier: 3.654A pdb=" N TYR F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 158 removed outlier: 3.812A pdb=" N GLU F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 150 " --> pdb=" O PHE F 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE A 12 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 46 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.650A pdb=" N GLY A 244 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 361 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 367 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.096A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) 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 703 through 705 removed outlier: 4.143A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 649 through 650 removed outlier: 5.961A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 876 through 878 Processing sheet with id=AB2, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.771A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 220 through 221 removed outlier: 6.607A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 375 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 399 removed outlier: 3.535A pdb=" N VAL B 397 " --> pdb=" O LYS B 441 " (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 479 through 480 removed outlier: 4.340A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.827A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE C 12 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 46 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.651A pdb=" N GLY C 244 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 361 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 367 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'C' and resid 372 through 374 Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AC7, first strand: chain 'C' and resid 479 through 480 removed outlier: 4.096A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) 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 703 through 705 removed outlier: 4.143A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 649 through 650 removed outlier: 5.962A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD3, first strand: chain 'C' and resid 889 through 890 Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.770A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 220 through 221 removed outlier: 6.608A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 375 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS D 379 " --> pdb=" O SER D 375 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 395 through 399 removed outlier: 3.534A pdb=" N VAL D 397 " --> pdb=" O LYS D 441 " (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 479 through 480 removed outlier: 4.340A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.827A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.08 - 0.51: 4 0.51 - 0.94: 0 0.94 - 1.36: 10295 1.36 - 1.79: 21401 1.79 - 2.22: 113 Warning: very small bond lengths. Bond restraints: 31813 Sorted by residual: bond pdb=" C27 AJP C1106 " pdb=" O78 AJP C1106 " ideal model delta sigma weight residual 1.406 0.083 1.323 2.00e-02 2.50e+03 4.38e+03 bond pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 1.406 0.151 1.255 2.00e-02 2.50e+03 3.94e+03 bond pdb=" C23 AJP A1106 " pdb=" O25 AJP A1106 " ideal model delta sigma weight residual 1.423 0.491 0.932 2.00e-02 2.50e+03 2.17e+03 bond pdb=" C23 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.423 0.495 0.928 2.00e-02 2.50e+03 2.15e+03 bond pdb=" C26 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.375 2.069 -0.694 2.00e-02 2.50e+03 1.21e+03 ... (remaining 31808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 41816 4.37 - 8.75: 948 8.75 - 13.12: 138 13.12 - 17.49: 12 17.49 - 21.87: 6 Bond angle restraints: 42920 Sorted by residual: angle pdb=" C ALA A 317 " pdb=" N ASN A 318 " pdb=" CA ASN A 318 " ideal model delta sigma weight residual 120.51 132.81 -12.30 1.45e+00 4.76e-01 7.20e+01 angle pdb=" C ALA C 317 " pdb=" N ASN C 318 " pdb=" CA ASN C 318 " ideal model delta sigma weight residual 120.51 132.75 -12.24 1.45e+00 4.76e-01 7.13e+01 angle pdb=" C17 CLR A1105 " pdb=" C13 CLR A1105 " pdb=" C18 CLR A1105 " ideal model delta sigma weight residual 110.18 88.31 21.87 3.00e+00 1.11e-01 5.31e+01 angle pdb=" C28 AJP A1106 " pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 108.61 129.29 -20.68 3.00e+00 1.11e-01 4.75e+01 angle pdb=" C04 AJP A1106 " pdb=" C05 AJP A1106 " pdb=" C06 AJP A1106 " ideal model delta sigma weight residual 114.54 134.46 -19.92 3.00e+00 1.11e-01 4.41e+01 ... (remaining 42915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.12: 18216 34.12 - 68.24: 413 68.24 - 102.36: 43 102.36 - 136.49: 7 136.49 - 170.61: 6 Dihedral angle restraints: 18685 sinusoidal: 7705 harmonic: 10980 Sorted by residual: dihedral pdb=" CA MET F 116 " pdb=" C MET F 116 " pdb=" N TYR F 117 " pdb=" CA TYR F 117 " ideal model delta harmonic sigma weight residual 180.00 120.45 59.55 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.51 59.49 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA VAL E 115 " pdb=" C VAL E 115 " pdb=" N MET E 116 " pdb=" CA MET E 116 " ideal model delta harmonic sigma weight residual 180.00 124.16 55.84 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 18682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.112: 4672 1.112 - 2.224: 3 2.224 - 3.336: 3 3.336 - 4.448: 7 4.448 - 5.560: 17 Chirality restraints: 4702 Sorted by residual: chirality pdb=" C02 AJP A1106 " pdb=" C01 AJP A1106 " pdb=" C03 AJP A1106 " pdb=" C85 AJP A1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C15 AJP A1106 " pdb=" C14 AJP A1106 " pdb=" C16 AJP A1106 " pdb=" C20 AJP A1106 " both_signs ideal model delta sigma weight residual False -2.42 3.14 -5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C02 AJP C1106 " pdb=" C01 AJP C1106 " pdb=" C03 AJP C1106 " pdb=" C85 AJP C1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.55 2.00e-01 2.50e+01 7.71e+02 ... (remaining 4699 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C MET F 116 " 0.066 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C MET E 116 " -0.066 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 193 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ILE A 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE A 193 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 194 " -0.022 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2907 2.72 - 3.27: 29904 3.27 - 3.81: 49802 3.81 - 4.36: 61352 4.36 - 4.90: 102405 Nonbonded interactions: 246370 Sorted by model distance: nonbonded pdb=" O25 AJP A1106 " pdb=" O79 AJP A1106 " model vdw 2.176 2.432 nonbonded pdb=" O25 AJP C1106 " pdb=" O79 AJP C1106 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP C1106 " pdb=" O78 AJP C1106 " model vdw 2.179 2.432 nonbonded pdb=" OE2 GLU A 755 " pdb=" OG1 THR D 482 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.223 3.040 ... (remaining 246365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 1110) selection = chain 'C' } ncs_group { reference = chain 'B' 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.025 1.323 31823 Z= 1.239 Angle : 1.637 21.867 42940 Z= 0.878 Chirality : 0.360 5.560 4702 Planarity : 0.007 0.064 5286 Dihedral : 14.413 170.608 11635 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.02 % Favored : 84.29 % Rotamer: Outliers : 0.80 % Allowed : 6.36 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.87 % 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: -5.79 (0.10), residues: 3762 helix: -3.79 (0.07), residues: 1714 sheet: -4.40 (0.21), residues: 370 loop : -3.65 (0.12), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 485 TYR 0.027 0.004 TYR A 702 PHE 0.052 0.004 PHE E 99 TRP 0.034 0.004 TRP C 861 HIS 0.012 0.003 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.02539 / 1.24 (31813) covalent geometry : angle 1.63617 / 0.88 (42920) SS BOND : bond 0.02044 / 1.50 ( 10) SS BOND : angle 3.29454 / 2.29 ( 20) hydrogen bonds : bond 0.29930 / 19.46 ( 1093) hydrogen bonds : angle 10.37714 / 7.13 ( 3201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 671 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8005 (ptm) cc_final: 0.7787 (ptp) REVERT: A 635 SER cc_start: 0.9024 (t) cc_final: 0.8818 (p) REVERT: A 638 ASP cc_start: 0.8386 (m-30) cc_final: 0.7982 (m-30) REVERT: A 879 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7829 (mmmt) REVERT: A 891 PHE cc_start: 0.8381 (m-10) cc_final: 0.7843 (m-10) REVERT: A 907 MET cc_start: 0.2736 (ppp) cc_final: 0.1586 (tpt) REVERT: A 922 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 939 MET cc_start: 0.8371 (ttm) cc_final: 0.7791 (tpt) REVERT: A 966 PHE cc_start: 0.6804 (m-80) cc_final: 0.6580 (m-80) REVERT: B 36 PHE cc_start: 0.6833 (t80) cc_final: 0.6079 (t80) REVERT: B 127 TYR cc_start: 0.8158 (t80) cc_final: 0.7942 (t80) REVERT: B 392 GLN cc_start: 0.7477 (mp10) cc_final: 0.7158 (mp10) REVERT: B 490 ASP cc_start: 0.7680 (m-30) cc_final: 0.7386 (p0) REVERT: B 573 ILE cc_start: 0.8779 (tp) cc_final: 0.8562 (tp) REVERT: B 626 VAL cc_start: 0.9240 (t) cc_final: 0.8655 (m) REVERT: C 414 MET cc_start: 0.8112 (ptm) cc_final: 0.7814 (ptp) REVERT: C 627 GLU cc_start: 0.8037 (pp20) cc_final: 0.7805 (pp20) REVERT: C 816 TYR cc_start: 0.7858 (t80) cc_final: 0.7443 (t80) REVERT: C 863 TYR cc_start: 0.6058 (m-10) cc_final: 0.5583 (m-10) REVERT: C 891 PHE cc_start: 0.8310 (m-10) cc_final: 0.7936 (m-80) REVERT: C 907 MET cc_start: 0.2477 (ppp) cc_final: 0.1857 (tpt) REVERT: C 966 PHE cc_start: 0.6975 (m-80) cc_final: 0.6484 (m-80) REVERT: D 36 PHE cc_start: 0.6737 (t80) cc_final: 0.6405 (t80) REVERT: D 392 GLN cc_start: 0.7302 (mp10) cc_final: 0.6923 (mp10) REVERT: D 440 TYR cc_start: 0.8443 (p90) cc_final: 0.8221 (p90) REVERT: D 490 ASP cc_start: 0.7713 (m-30) cc_final: 0.7477 (p0) REVERT: E 67 LEU cc_start: 0.7897 (mt) cc_final: 0.7696 (mm) REVERT: E 88 TRP cc_start: 0.5912 (m100) cc_final: 0.5264 (t60) REVERT: F 88 TRP cc_start: 0.5698 (m100) cc_final: 0.5161 (t60) outliers start: 26 outliers final: 4 residues processed: 692 average time/residue: 0.2057 time to fit residues: 229.4867 Evaluate side-chains 379 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 374 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 60 ASN A 167 ASN A 202 ASN A 344 ASN A 575 ASN A 764 ASN A 950 HIS A 985 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 60 ASN B 219 HIS B 224 ASN B 311 ASN B 318 ASN B 344 ASN B 350 ASN B 461 ASN B 508 GLN C 46 HIS C 60 ASN C 147 GLN C 167 ASN C 202 ASN C 344 ASN C 575 ASN C 726 ASN C 764 ASN C 950 HIS C 985 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS D 224 ASN D 311 ASN D 318 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 461 ASN E 129 ASN F 129 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106847 restraints weight = 54814.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108978 restraints weight = 39756.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109189 restraints weight = 37870.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110486 restraints weight = 25314.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111173 restraints weight = 21982.337| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31823 Z= 0.177 Angle : 0.983 31.549 42940 Z= 0.449 Chirality : 0.087 2.230 4702 Planarity : 0.005 0.058 5286 Dihedral : 14.156 162.525 4636 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.59 % Favored : 87.96 % Rotamer: Outliers : 2.79 % Allowed : 11.09 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.12), residues: 3762 helix: -1.89 (0.11), residues: 1778 sheet: -4.03 (0.23), residues: 390 loop : -3.31 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 692 TYR 0.031 0.002 TYR C1001 PHE 0.029 0.002 PHE C 517 TRP 0.016 0.001 TRP D 766 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (31813) covalent geometry : angle 0.98172 / 0.45 (42920) SS BOND : bond 0.00398 / 0.24 ( 10) SS BOND : angle 2.53821 / 1.13 ( 20) hydrogen bonds : bond 0.04775 / 3.12 ( 1093) hydrogen bonds : angle 5.27295 / 3.67 ( 3201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 480 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8864 (pt) cc_final: 0.8638 (pt) REVERT: A 186 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8623 (pp) REVERT: A 302 GLN cc_start: 0.7550 (pm20) cc_final: 0.7309 (mp10) REVERT: A 414 MET cc_start: 0.7776 (ptm) cc_final: 0.7560 (ptp) REVERT: A 463 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: A 638 ASP cc_start: 0.8390 (m-30) cc_final: 0.8063 (m-30) REVERT: A 879 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7925 (mmmt) REVERT: A 891 PHE cc_start: 0.8470 (m-10) cc_final: 0.8090 (m-10) REVERT: A 901 PHE cc_start: 0.6844 (m-80) cc_final: 0.6429 (m-10) REVERT: A 939 MET cc_start: 0.7712 (ttm) cc_final: 0.7459 (tpt) REVERT: A 966 PHE cc_start: 0.6925 (m-80) cc_final: 0.6535 (m-80) REVERT: A 1005 TRP cc_start: 0.7183 (p-90) cc_final: 0.6894 (p-90) REVERT: B 46 HIS cc_start: 0.7392 (t-90) cc_final: 0.7026 (t-170) REVERT: B 114 ARG cc_start: 0.8514 (ttm170) cc_final: 0.8253 (ttm170) REVERT: B 133 PHE cc_start: 0.8809 (m-10) cc_final: 0.8416 (m-10) REVERT: B 357 THR cc_start: 0.7984 (p) cc_final: 0.7573 (t) REVERT: B 361 MET cc_start: 0.8159 (mtp) cc_final: 0.7813 (mtp) REVERT: B 392 GLN cc_start: 0.7668 (mp10) cc_final: 0.7308 (mp10) REVERT: B 527 MET cc_start: 0.7628 (tpp) cc_final: 0.7330 (mmt) REVERT: B 573 ILE cc_start: 0.8760 (tp) cc_final: 0.8505 (tp) REVERT: C 50 LEU cc_start: 0.8721 (pt) cc_final: 0.8419 (pt) REVERT: C 302 GLN cc_start: 0.7566 (pm20) cc_final: 0.7248 (mp10) REVERT: C 412 HIS cc_start: 0.7356 (t-170) cc_final: 0.7063 (t70) REVERT: C 414 MET cc_start: 0.7796 (ptm) cc_final: 0.7562 (ptp) REVERT: C 627 GLU cc_start: 0.8196 (pp20) cc_final: 0.7705 (tm-30) REVERT: C 635 SER cc_start: 0.8988 (t) cc_final: 0.8757 (p) REVERT: C 816 TYR cc_start: 0.7789 (t80) cc_final: 0.7448 (t80) REVERT: C 863 TYR cc_start: 0.5994 (m-10) cc_final: 0.5405 (m-10) REVERT: C 891 PHE cc_start: 0.8322 (m-10) cc_final: 0.8047 (m-80) REVERT: C 907 MET cc_start: 0.2067 (ppp) cc_final: 0.1476 (tpt) REVERT: C 966 PHE cc_start: 0.7039 (m-80) cc_final: 0.6416 (m-80) REVERT: D 33 MET cc_start: 0.8722 (ptm) cc_final: 0.8463 (ptt) REVERT: D 269 GLU cc_start: 0.7592 (tp30) cc_final: 0.7082 (tp30) REVERT: D 357 THR cc_start: 0.7776 (p) cc_final: 0.7521 (t) REVERT: D 373 TYR cc_start: 0.8897 (p90) cc_final: 0.8654 (p90) REVERT: D 392 GLN cc_start: 0.7480 (mp10) cc_final: 0.7065 (mp10) REVERT: D 408 MET cc_start: 0.7161 (mmm) cc_final: 0.5443 (mmm) REVERT: D 585 MET cc_start: 0.8761 (mmt) cc_final: 0.7701 (mmt) REVERT: D 773 CYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7530 (m) REVERT: E 88 TRP cc_start: 0.6537 (m100) cc_final: 0.5478 (t60) REVERT: E 116 MET cc_start: 0.1244 (tpp) cc_final: 0.0055 (pmm) REVERT: E 117 TYR cc_start: 0.1438 (m-80) cc_final: -0.1369 (m-80) REVERT: F 84 CYS cc_start: 0.8041 (m) cc_final: 0.7822 (m) REVERT: F 88 TRP cc_start: 0.6449 (m100) cc_final: 0.5494 (t60) REVERT: F 116 MET cc_start: 0.0638 (tpp) cc_final: 0.0105 (pmm) outliers start: 91 outliers final: 33 residues processed: 541 average time/residue: 0.1918 time to fit residues: 174.0371 Evaluate side-chains 414 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 378 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 13 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 311 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 309 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 167 ASN A 726 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 112 GLN C 985 ASN D 24 GLN D 112 GLN D 412 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.142426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106019 restraints weight = 54694.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107067 restraints weight = 38277.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107374 restraints weight = 39837.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108499 restraints weight = 26078.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109339 restraints weight = 22776.099| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 31823 Z= 0.153 Angle : 0.911 31.491 42940 Z= 0.412 Chirality : 0.085 2.295 4702 Planarity : 0.004 0.053 5286 Dihedral : 13.412 155.830 4632 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.32 % Favored : 88.28 % Rotamer: Outliers : 2.76 % Allowed : 13.45 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.13), residues: 3762 helix: -1.05 (0.12), residues: 1780 sheet: -3.89 (0.24), residues: 352 loop : -3.06 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 65 TYR 0.025 0.002 TYR C1001 PHE 0.020 0.001 PHE C 517 TRP 0.014 0.001 TRP A 887 HIS 0.011 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31813) covalent geometry : angle 0.90952 / 0.41 (42920) SS BOND : bond 0.00317 / 0.18 ( 10) SS BOND : angle 2.48495 / 1.31 ( 20) hydrogen bonds : bond 0.04216 / 2.77 ( 1093) hydrogen bonds : angle 4.72072 / 3.26 ( 3201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 409 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7555 (ptm160) REVERT: A 50 LEU cc_start: 0.8766 (pt) cc_final: 0.8527 (pt) REVERT: A 262 TRP cc_start: 0.8458 (t-100) cc_final: 0.8164 (t-100) REVERT: A 414 MET cc_start: 0.7795 (ptm) cc_final: 0.7595 (ptp) REVERT: A 638 ASP cc_start: 0.8286 (m-30) cc_final: 0.7874 (t0) REVERT: A 879 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7903 (mmmt) REVERT: A 891 PHE cc_start: 0.8475 (m-10) cc_final: 0.8262 (m-80) REVERT: A 901 PHE cc_start: 0.6820 (m-80) cc_final: 0.6372 (m-10) REVERT: A 907 MET cc_start: 0.1857 (OUTLIER) cc_final: 0.1153 (tpt) REVERT: A 924 MET cc_start: 0.7425 (pmm) cc_final: 0.7127 (pmm) REVERT: A 939 MET cc_start: 0.7597 (ttm) cc_final: 0.7287 (tpt) REVERT: A 966 PHE cc_start: 0.6923 (m-80) cc_final: 0.6468 (m-80) REVERT: A 988 MET cc_start: 0.8236 (tmm) cc_final: 0.7648 (tmm) REVERT: A 1005 TRP cc_start: 0.7234 (p-90) cc_final: 0.6918 (p-90) REVERT: B 33 MET cc_start: 0.8657 (ptm) cc_final: 0.8354 (ptt) REVERT: B 74 PHE cc_start: 0.8105 (t80) cc_final: 0.7847 (t80) REVERT: B 189 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 357 THR cc_start: 0.7911 (p) cc_final: 0.7602 (t) REVERT: B 361 MET cc_start: 0.8180 (mtp) cc_final: 0.7874 (mtp) REVERT: B 392 GLN cc_start: 0.7726 (mp10) cc_final: 0.7358 (mp10) REVERT: B 408 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.5911 (mmm) REVERT: B 527 MET cc_start: 0.7646 (tpp) cc_final: 0.7281 (mmt) REVERT: B 573 ILE cc_start: 0.8744 (tp) cc_final: 0.8489 (tp) REVERT: C 42 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7718 (ptm160) REVERT: C 50 LEU cc_start: 0.8611 (pt) cc_final: 0.8296 (pt) REVERT: C 414 MET cc_start: 0.7868 (ptm) cc_final: 0.7517 (ptp) REVERT: C 585 MET cc_start: 0.8148 (mpt) cc_final: 0.7889 (mpt) REVERT: C 627 GLU cc_start: 0.8109 (pp20) cc_final: 0.7783 (tm-30) REVERT: C 635 SER cc_start: 0.9013 (t) cc_final: 0.8792 (p) REVERT: C 816 TYR cc_start: 0.7793 (t80) cc_final: 0.7483 (t80) REVERT: C 863 TYR cc_start: 0.5959 (m-10) cc_final: 0.5295 (m-10) REVERT: C 891 PHE cc_start: 0.8372 (m-10) cc_final: 0.8091 (m-80) REVERT: C 907 MET cc_start: 0.2191 (ppp) cc_final: 0.1434 (tpt) REVERT: C 924 MET cc_start: 0.7321 (ptp) cc_final: 0.6802 (mtm) REVERT: C 966 PHE cc_start: 0.7130 (m-80) cc_final: 0.6459 (m-80) REVERT: C 985 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.6920 (p0) REVERT: C 1002 LYS cc_start: 0.7266 (ttmp) cc_final: 0.6689 (mtmt) REVERT: D 33 MET cc_start: 0.8610 (ptm) cc_final: 0.8350 (ptt) REVERT: D 133 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8558 (m-10) REVERT: D 189 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7131 (mm-30) REVERT: D 361 MET cc_start: 0.8122 (mtp) cc_final: 0.7834 (mtp) REVERT: D 392 GLN cc_start: 0.7476 (mp10) cc_final: 0.7156 (mp10) REVERT: D 527 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6900 (mmt) REVERT: D 585 MET cc_start: 0.8795 (mmt) cc_final: 0.8286 (mmm) REVERT: E 81 MET cc_start: 0.8670 (ttt) cc_final: 0.8463 (tmm) REVERT: E 88 TRP cc_start: 0.6624 (m100) cc_final: 0.5589 (t60) REVERT: E 116 MET cc_start: 0.0790 (tpp) cc_final: 0.0166 (pmm) REVERT: E 122 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6699 (mm) REVERT: F 88 TRP cc_start: 0.6519 (m100) cc_final: 0.5589 (t60) REVERT: F 116 MET cc_start: 0.0686 (tpp) cc_final: -0.0165 (pmm) outliers start: 90 outliers final: 41 residues processed: 469 average time/residue: 0.1890 time to fit residues: 147.9261 Evaluate side-chains 406 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 54 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 242 optimal weight: 0.4980 chunk 316 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102975 restraints weight = 54565.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103593 restraints weight = 39144.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103508 restraints weight = 44607.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104795 restraints weight = 27910.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106241 restraints weight = 23792.993| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31823 Z= 0.226 Angle : 0.918 31.895 42940 Z= 0.417 Chirality : 0.086 2.284 4702 Planarity : 0.004 0.057 5286 Dihedral : 12.977 147.388 4630 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.25 % Favored : 87.37 % Rotamer: Outliers : 2.95 % Allowed : 14.10 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.13), residues: 3762 helix: -0.67 (0.12), residues: 1782 sheet: -3.76 (0.24), residues: 360 loop : -3.00 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 141 TYR 0.026 0.002 TYR C1001 PHE 0.022 0.002 PHE C 495 TRP 0.012 0.001 TRP F 136 HIS 0.013 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (31813) covalent geometry : angle 0.91748 / 0.42 (42920) SS BOND : bond 0.00397 / 0.25 ( 10) SS BOND : angle 1.84853 / 1.08 ( 20) hydrogen bonds : bond 0.04015 / 2.64 ( 1093) hydrogen bonds : angle 4.61099 / 3.17 ( 3201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 380 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8815 (pt) cc_final: 0.8550 (pt) REVERT: A 414 MET cc_start: 0.7818 (ptm) cc_final: 0.7588 (ptp) REVERT: A 642 GLN cc_start: 0.7545 (mp10) cc_final: 0.7262 (mp10) REVERT: A 879 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7957 (mmmt) REVERT: A 891 PHE cc_start: 0.8466 (m-10) cc_final: 0.8177 (m-80) REVERT: A 907 MET cc_start: 0.1834 (OUTLIER) cc_final: 0.1024 (tpt) REVERT: A 939 MET cc_start: 0.7675 (ttm) cc_final: 0.7392 (tpt) REVERT: A 966 PHE cc_start: 0.6931 (m-80) cc_final: 0.6532 (m-80) REVERT: A 988 MET cc_start: 0.8254 (tmm) cc_final: 0.8000 (tmm) REVERT: A 1005 TRP cc_start: 0.7239 (p-90) cc_final: 0.6896 (p-90) REVERT: A 1029 MET cc_start: 0.7581 (mmt) cc_final: 0.7188 (tpp) REVERT: B 133 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: B 189 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 357 THR cc_start: 0.8029 (p) cc_final: 0.7709 (t) REVERT: B 361 MET cc_start: 0.8287 (mtp) cc_final: 0.7972 (mtp) REVERT: B 392 GLN cc_start: 0.7734 (mp10) cc_final: 0.7389 (mp10) REVERT: B 408 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.5794 (mmm) REVERT: B 527 MET cc_start: 0.7700 (tpp) cc_final: 0.7318 (mmt) REVERT: B 573 ILE cc_start: 0.8757 (tp) cc_final: 0.8498 (tp) REVERT: B 585 MET cc_start: 0.8894 (mmt) cc_final: 0.8244 (mmt) REVERT: B 814 PHE cc_start: 0.7192 (t80) cc_final: 0.6966 (t80) REVERT: C 50 LEU cc_start: 0.8711 (pt) cc_final: 0.8384 (pt) REVERT: C 262 TRP cc_start: 0.8371 (t-100) cc_final: 0.8126 (t-100) REVERT: C 414 MET cc_start: 0.7929 (ptm) cc_final: 0.7589 (ptp) REVERT: C 627 GLU cc_start: 0.8293 (pp20) cc_final: 0.8031 (tm-30) REVERT: C 721 MET cc_start: 0.8161 (ptt) cc_final: 0.7884 (ptt) REVERT: C 863 TYR cc_start: 0.6121 (m-10) cc_final: 0.5518 (m-10) REVERT: C 891 PHE cc_start: 0.8410 (m-10) cc_final: 0.8116 (m-80) REVERT: C 907 MET cc_start: 0.2104 (ppp) cc_final: 0.1244 (tpt) REVERT: C 924 MET cc_start: 0.7491 (ptp) cc_final: 0.6896 (mtm) REVERT: C 966 PHE cc_start: 0.6980 (m-80) cc_final: 0.6410 (m-80) REVERT: C 1002 LYS cc_start: 0.7374 (ttmp) cc_final: 0.6807 (mtmt) REVERT: C 1009 PHE cc_start: 0.7438 (m-80) cc_final: 0.7023 (t80) REVERT: D 133 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8647 (m-10) REVERT: D 189 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 248 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7482 (t) REVERT: D 361 MET cc_start: 0.8271 (mtp) cc_final: 0.7978 (mtp) REVERT: D 515 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: D 527 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7012 (mmt) REVERT: D 585 MET cc_start: 0.8894 (mmt) cc_final: 0.8394 (mmm) REVERT: E 81 MET cc_start: 0.8952 (ttt) cc_final: 0.8619 (tmm) REVERT: E 88 TRP cc_start: 0.6615 (m100) cc_final: 0.5683 (t60) REVERT: E 115 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6208 (m) REVERT: E 116 MET cc_start: 0.1077 (tpp) cc_final: 0.0107 (pmm) REVERT: F 88 TRP cc_start: 0.6546 (m100) cc_final: 0.5662 (t60) REVERT: F 116 MET cc_start: 0.0538 (tpp) cc_final: -0.0387 (pmm) outliers start: 96 outliers final: 62 residues processed: 445 average time/residue: 0.1897 time to fit residues: 141.1897 Evaluate side-chains 416 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 346 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 700 TYR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 124 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 348 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS C 335 GLN C 985 ASN D 13 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.142557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105447 restraints weight = 54479.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105536 restraints weight = 36137.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106045 restraints weight = 37768.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107054 restraints weight = 25979.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107735 restraints weight = 23066.453| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31823 Z= 0.121 Angle : 0.860 31.557 42940 Z= 0.382 Chirality : 0.084 2.235 4702 Planarity : 0.004 0.042 5286 Dihedral : 12.377 143.628 4630 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.98 % Favored : 88.78 % Rotamer: Outliers : 2.43 % Allowed : 15.57 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 3762 helix: -0.22 (0.12), residues: 1782 sheet: -3.71 (0.23), residues: 384 loop : -2.82 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 888 TYR 0.026 0.001 TYR C1001 PHE 0.019 0.001 PHE D 515 TRP 0.018 0.001 TRP A 262 HIS 0.005 0.001 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (31813) covalent geometry : angle 0.85924 / 0.38 (42920) SS BOND : bond 0.00200 / 0.10 ( 10) SS BOND : angle 1.50788 / 0.80 ( 20) hydrogen bonds : bond 0.03495 / 2.30 ( 1093) hydrogen bonds : angle 4.29004 / 2.95 ( 3201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 401 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8520 (pt) cc_final: 0.8255 (pt) REVERT: A 414 MET cc_start: 0.7780 (ptm) cc_final: 0.7548 (ptp) REVERT: A 642 GLN cc_start: 0.7523 (mp10) cc_final: 0.7165 (mp10) REVERT: A 879 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7874 (mmmt) REVERT: A 891 PHE cc_start: 0.8442 (m-10) cc_final: 0.8173 (m-80) REVERT: A 966 PHE cc_start: 0.6943 (m-80) cc_final: 0.6535 (m-80) REVERT: A 988 MET cc_start: 0.8174 (tmm) cc_final: 0.7891 (tmm) REVERT: A 1005 TRP cc_start: 0.7189 (p-90) cc_final: 0.6965 (p-90) REVERT: B 189 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6935 (mm-30) REVERT: B 357 THR cc_start: 0.7865 (p) cc_final: 0.7550 (t) REVERT: B 361 MET cc_start: 0.8285 (mtp) cc_final: 0.7744 (mtp) REVERT: B 392 GLN cc_start: 0.7659 (mp10) cc_final: 0.7388 (mp10) REVERT: B 408 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5952 (mmt) REVERT: B 515 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: B 573 ILE cc_start: 0.8609 (tp) cc_final: 0.8351 (tp) REVERT: B 585 MET cc_start: 0.8799 (mmt) cc_final: 0.8314 (mmt) REVERT: B 814 PHE cc_start: 0.7230 (t80) cc_final: 0.6957 (t80) REVERT: C 189 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8014 (tp30) REVERT: C 414 MET cc_start: 0.7872 (ptm) cc_final: 0.7534 (ptp) REVERT: C 721 MET cc_start: 0.8048 (ptt) cc_final: 0.7824 (ptt) REVERT: C 863 TYR cc_start: 0.6093 (m-10) cc_final: 0.5545 (m-10) REVERT: C 891 PHE cc_start: 0.8386 (m-10) cc_final: 0.8014 (m-10) REVERT: C 907 MET cc_start: 0.1955 (ppp) cc_final: 0.1024 (tpt) REVERT: C 966 PHE cc_start: 0.7044 (m-80) cc_final: 0.6458 (m-80) REVERT: C 985 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.6950 (p0) REVERT: C 1002 LYS cc_start: 0.7339 (ttmp) cc_final: 0.6768 (mtmt) REVERT: C 1009 PHE cc_start: 0.7470 (m-80) cc_final: 0.7093 (t80) REVERT: D 36 PHE cc_start: 0.7059 (t80) cc_final: 0.6539 (t80) REVERT: D 133 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8248 (m-10) REVERT: D 189 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7017 (mm-30) REVERT: D 248 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7320 (t) REVERT: D 361 MET cc_start: 0.8269 (mtp) cc_final: 0.7899 (mtp) REVERT: D 498 LEU cc_start: 0.9053 (pt) cc_final: 0.8442 (pt) REVERT: D 515 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: D 527 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7049 (mmt) REVERT: D 585 MET cc_start: 0.8796 (mmt) cc_final: 0.8306 (mmt) REVERT: E 81 MET cc_start: 0.8942 (ttt) cc_final: 0.8622 (tmm) REVERT: E 88 TRP cc_start: 0.6617 (m100) cc_final: 0.5734 (t60) REVERT: E 115 VAL cc_start: 0.6327 (OUTLIER) cc_final: 0.5984 (m) REVERT: E 116 MET cc_start: 0.1082 (tpp) cc_final: 0.0313 (pmm) REVERT: E 122 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6320 (mm) REVERT: F 10 TYR cc_start: 0.8082 (m-80) cc_final: 0.7364 (m-10) REVERT: F 88 TRP cc_start: 0.6539 (m100) cc_final: 0.5689 (t60) REVERT: F 115 VAL cc_start: 0.6437 (OUTLIER) cc_final: 0.6118 (m) REVERT: F 116 MET cc_start: 0.0552 (tpp) cc_final: -0.0440 (pmm) REVERT: F 122 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6361 (tp) outliers start: 79 outliers final: 47 residues processed: 451 average time/residue: 0.1835 time to fit residues: 138.6035 Evaluate side-chains 398 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 77 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 318 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 246 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.142428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105564 restraints weight = 54444.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105536 restraints weight = 36322.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105995 restraints weight = 38284.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107133 restraints weight = 26352.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108114 restraints weight = 23210.541| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31823 Z= 0.134 Angle : 0.861 31.557 42940 Z= 0.382 Chirality : 0.084 2.217 4702 Planarity : 0.004 0.038 5286 Dihedral : 12.065 145.059 4630 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.95 % Favored : 88.78 % Rotamer: Outliers : 2.76 % Allowed : 16.31 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.14), residues: 3762 helix: 0.04 (0.13), residues: 1780 sheet: -3.52 (0.24), residues: 358 loop : -2.78 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.026 0.001 TYR C1001 PHE 0.029 0.001 PHE D 517 TRP 0.022 0.001 TRP C 262 HIS 0.011 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (31813) covalent geometry : angle 0.86092 / 0.38 (42920) SS BOND : bond 0.00239 / 0.12 ( 10) SS BOND : angle 1.55655 / 0.89 ( 20) hydrogen bonds : bond 0.03404 / 2.25 ( 1093) hydrogen bonds : angle 4.19170 / 2.87 ( 3201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8445 (pt) cc_final: 0.8165 (pt) REVERT: A 414 MET cc_start: 0.7755 (ptm) cc_final: 0.7535 (ptp) REVERT: A 642 GLN cc_start: 0.7519 (mp10) cc_final: 0.7138 (mp10) REVERT: A 879 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7852 (mmmt) REVERT: A 891 PHE cc_start: 0.8411 (m-10) cc_final: 0.8166 (m-80) REVERT: A 939 MET cc_start: 0.7533 (tpt) cc_final: 0.7058 (ttt) REVERT: A 966 PHE cc_start: 0.7062 (m-80) cc_final: 0.6358 (m-80) REVERT: A 988 MET cc_start: 0.8141 (tmm) cc_final: 0.7803 (tmm) REVERT: A 1009 PHE cc_start: 0.7798 (m-80) cc_final: 0.7516 (t80) REVERT: B 189 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 357 THR cc_start: 0.7929 (p) cc_final: 0.7601 (t) REVERT: B 361 MET cc_start: 0.8253 (mtp) cc_final: 0.7693 (mtp) REVERT: B 404 PRO cc_start: 0.8281 (Cg_exo) cc_final: 0.8046 (Cg_endo) REVERT: B 425 CYS cc_start: 0.7157 (m) cc_final: 0.6953 (m) REVERT: B 515 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: B 573 ILE cc_start: 0.8594 (tp) cc_final: 0.8337 (tp) REVERT: B 585 MET cc_start: 0.8832 (mmt) cc_final: 0.8400 (mmt) REVERT: B 695 LYS cc_start: 0.7879 (pttp) cc_final: 0.7650 (pttp) REVERT: B 814 PHE cc_start: 0.7258 (t80) cc_final: 0.6820 (t80) REVERT: C 189 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8036 (tp30) REVERT: C 414 MET cc_start: 0.7883 (ptm) cc_final: 0.7558 (ptp) REVERT: C 638 ASP cc_start: 0.8330 (m-30) cc_final: 0.7538 (t0) REVERT: C 721 MET cc_start: 0.7999 (ptt) cc_final: 0.7751 (ptt) REVERT: C 863 TYR cc_start: 0.6081 (m-10) cc_final: 0.5443 (m-10) REVERT: C 891 PHE cc_start: 0.8347 (m-10) cc_final: 0.8082 (m-10) REVERT: C 907 MET cc_start: 0.2293 (ppp) cc_final: 0.1220 (tpt) REVERT: C 924 MET cc_start: 0.7550 (ptp) cc_final: 0.6888 (mtm) REVERT: C 966 PHE cc_start: 0.7016 (m-80) cc_final: 0.6457 (m-80) REVERT: C 1002 LYS cc_start: 0.7382 (ttmp) cc_final: 0.6805 (mtmt) REVERT: C 1009 PHE cc_start: 0.7365 (m-80) cc_final: 0.7092 (t80) REVERT: D 133 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8325 (m-10) REVERT: D 189 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7045 (mm-30) REVERT: D 248 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7317 (t) REVERT: D 361 MET cc_start: 0.8300 (mtp) cc_final: 0.7881 (mtp) REVERT: D 515 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: D 527 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7074 (mmt) REVERT: D 585 MET cc_start: 0.8817 (mmt) cc_final: 0.8460 (mmt) REVERT: E 81 MET cc_start: 0.8943 (ttt) cc_final: 0.8596 (tmm) REVERT: E 88 TRP cc_start: 0.6583 (m100) cc_final: 0.5723 (t60) REVERT: E 115 VAL cc_start: 0.6169 (OUTLIER) cc_final: 0.5842 (m) REVERT: E 116 MET cc_start: 0.0872 (tpp) cc_final: 0.0260 (pmm) REVERT: E 122 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6347 (mm) REVERT: F 66 LYS cc_start: 0.7422 (mttt) cc_final: 0.7072 (mttm) REVERT: F 88 TRP cc_start: 0.6458 (m100) cc_final: 0.5557 (t60) REVERT: F 115 VAL cc_start: 0.6178 (OUTLIER) cc_final: 0.5877 (m) REVERT: F 116 MET cc_start: 0.0677 (tpp) cc_final: -0.0298 (pmm) outliers start: 90 outliers final: 53 residues processed: 429 average time/residue: 0.1772 time to fit residues: 127.5281 Evaluate side-chains 393 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 332 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 354 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 954 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105791 restraints weight = 54531.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106446 restraints weight = 39737.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106911 restraints weight = 40137.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108441 restraints weight = 26330.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109192 restraints weight = 22418.376| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31823 Z= 0.141 Angle : 0.857 31.564 42940 Z= 0.379 Chirality : 0.084 2.208 4702 Planarity : 0.003 0.036 5286 Dihedral : 11.809 144.519 4630 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.71 % Favored : 89.02 % Rotamer: Outliers : 2.58 % Allowed : 16.74 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.14), residues: 3762 helix: 0.16 (0.13), residues: 1794 sheet: -3.38 (0.24), residues: 378 loop : -2.76 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 888 TYR 0.025 0.001 TYR C1001 PHE 0.031 0.001 PHE A 937 TRP 0.020 0.001 TRP C 262 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31813) covalent geometry : angle 0.85669 / 0.38 (42920) SS BOND : bond 0.00241 / 0.13 ( 10) SS BOND : angle 1.56664 / 0.90 ( 20) hydrogen bonds : bond 0.03335 / 2.21 ( 1093) hydrogen bonds : angle 4.16375 / 2.85 ( 3201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 355 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8368 (pt) cc_final: 0.8053 (pt) REVERT: A 412 HIS cc_start: 0.7091 (t-170) cc_final: 0.6774 (t70) REVERT: A 414 MET cc_start: 0.7794 (ptm) cc_final: 0.7561 (ptp) REVERT: A 642 GLN cc_start: 0.7510 (mp10) cc_final: 0.7082 (mp10) REVERT: A 678 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 879 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7909 (mmmt) REVERT: A 891 PHE cc_start: 0.8430 (m-10) cc_final: 0.8140 (m-80) REVERT: A 939 MET cc_start: 0.7460 (tpt) cc_final: 0.6986 (ttm) REVERT: A 966 PHE cc_start: 0.6997 (m-80) cc_final: 0.6358 (m-80) REVERT: A 988 MET cc_start: 0.8081 (tmm) cc_final: 0.7740 (tmm) REVERT: B 41 PHE cc_start: 0.5091 (OUTLIER) cc_final: 0.3749 (p90) REVERT: B 189 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6956 (mm-30) REVERT: B 357 THR cc_start: 0.7951 (p) cc_final: 0.7633 (t) REVERT: B 361 MET cc_start: 0.8237 (mtp) cc_final: 0.7695 (mtp) REVERT: B 515 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: B 573 ILE cc_start: 0.8488 (tp) cc_final: 0.8200 (tp) REVERT: B 585 MET cc_start: 0.8803 (mmt) cc_final: 0.8340 (mmt) REVERT: B 695 LYS cc_start: 0.7811 (pttp) cc_final: 0.7604 (pttp) REVERT: B 814 PHE cc_start: 0.7264 (t80) cc_final: 0.6810 (t80) REVERT: C 189 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7900 (tp30) REVERT: C 414 MET cc_start: 0.7886 (ptm) cc_final: 0.7567 (ptp) REVERT: C 638 ASP cc_start: 0.8291 (m-30) cc_final: 0.7605 (t70) REVERT: C 721 MET cc_start: 0.7948 (ptt) cc_final: 0.7747 (ptt) REVERT: C 860 TYR cc_start: 0.7880 (m-80) cc_final: 0.7563 (m-10) REVERT: C 863 TYR cc_start: 0.6120 (m-10) cc_final: 0.5584 (m-10) REVERT: C 891 PHE cc_start: 0.8405 (m-10) cc_final: 0.8161 (m-10) REVERT: C 907 MET cc_start: 0.2180 (ppp) cc_final: 0.1212 (tpt) REVERT: C 966 PHE cc_start: 0.7023 (m-80) cc_final: 0.6530 (m-80) REVERT: C 1002 LYS cc_start: 0.7426 (ttmp) cc_final: 0.6898 (mtmt) REVERT: C 1009 PHE cc_start: 0.7355 (m-80) cc_final: 0.7093 (t80) REVERT: D 133 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8348 (m-10) REVERT: D 189 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 361 MET cc_start: 0.8295 (mtp) cc_final: 0.7907 (mtp) REVERT: D 515 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: D 527 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7081 (mmt) REVERT: D 585 MET cc_start: 0.8813 (mmt) cc_final: 0.8492 (mmt) REVERT: E 81 MET cc_start: 0.8965 (ttt) cc_final: 0.8607 (tmm) REVERT: E 88 TRP cc_start: 0.6544 (m100) cc_final: 0.5711 (t60) REVERT: E 115 VAL cc_start: 0.6055 (OUTLIER) cc_final: 0.5802 (m) REVERT: E 116 MET cc_start: 0.0598 (tpp) cc_final: 0.0032 (pmm) REVERT: E 122 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6066 (mm) REVERT: F 88 TRP cc_start: 0.6418 (m100) cc_final: 0.5602 (t60) REVERT: F 115 VAL cc_start: 0.6020 (OUTLIER) cc_final: 0.5738 (m) REVERT: F 116 MET cc_start: 0.0589 (tpp) cc_final: -0.0263 (pmm) outliers start: 84 outliers final: 55 residues processed: 415 average time/residue: 0.1763 time to fit residues: 124.2225 Evaluate side-chains 390 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 327 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 8 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 190 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 107 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106147 restraints weight = 54263.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105462 restraints weight = 38079.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106534 restraints weight = 35553.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106799 restraints weight = 27763.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107730 restraints weight = 24598.794| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31823 Z= 0.127 Angle : 0.856 31.472 42940 Z= 0.375 Chirality : 0.083 2.196 4702 Planarity : 0.003 0.035 5286 Dihedral : 11.593 144.090 4630 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.79 % Favored : 88.97 % Rotamer: Outliers : 2.24 % Allowed : 17.44 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.98 (0.14), residues: 3762 helix: 0.29 (0.13), residues: 1802 sheet: -3.28 (0.25), residues: 368 loop : -2.77 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 888 TYR 0.024 0.001 TYR C1001 PHE 0.028 0.001 PHE A 937 TRP 0.019 0.001 TRP A 262 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (31813) covalent geometry : angle 0.85571 / 0.38 (42920) SS BOND : bond 0.00331 / 0.17 ( 10) SS BOND : angle 1.60785 / 0.92 ( 20) hydrogen bonds : bond 0.03253 / 2.15 ( 1093) hydrogen bonds : angle 4.13820 / 2.83 ( 3201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 346 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8253 (pt) cc_final: 0.7950 (pt) REVERT: A 414 MET cc_start: 0.7850 (ptm) cc_final: 0.7592 (ptp) REVERT: A 638 ASP cc_start: 0.8298 (m-30) cc_final: 0.7510 (t0) REVERT: A 642 GLN cc_start: 0.7521 (mp10) cc_final: 0.6964 (mp10) REVERT: A 879 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7847 (mmmt) REVERT: A 891 PHE cc_start: 0.8369 (m-10) cc_final: 0.8097 (m-80) REVERT: A 939 MET cc_start: 0.7452 (tpt) cc_final: 0.6950 (ttm) REVERT: A 966 PHE cc_start: 0.7038 (m-80) cc_final: 0.6388 (m-80) REVERT: A 988 MET cc_start: 0.8008 (tmm) cc_final: 0.7656 (tmm) REVERT: A 1009 PHE cc_start: 0.7795 (t80) cc_final: 0.7569 (t80) REVERT: B 41 PHE cc_start: 0.4969 (OUTLIER) cc_final: 0.3735 (p90) REVERT: B 189 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 303 ARG cc_start: 0.7149 (mmm160) cc_final: 0.6946 (mmp80) REVERT: B 357 THR cc_start: 0.7927 (p) cc_final: 0.7604 (t) REVERT: B 361 MET cc_start: 0.8235 (mtp) cc_final: 0.7693 (mtp) REVERT: B 404 PRO cc_start: 0.8280 (Cg_exo) cc_final: 0.7976 (Cg_endo) REVERT: B 515 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: B 573 ILE cc_start: 0.8438 (tp) cc_final: 0.8129 (tp) REVERT: B 585 MET cc_start: 0.8792 (mmt) cc_final: 0.8417 (mmt) REVERT: B 814 PHE cc_start: 0.7259 (t80) cc_final: 0.6816 (t80) REVERT: C 414 MET cc_start: 0.7898 (ptm) cc_final: 0.7573 (ptp) REVERT: C 721 MET cc_start: 0.7958 (ptt) cc_final: 0.7749 (ptt) REVERT: C 860 TYR cc_start: 0.7873 (m-80) cc_final: 0.7538 (m-10) REVERT: C 863 TYR cc_start: 0.6127 (m-10) cc_final: 0.5559 (m-10) REVERT: C 891 PHE cc_start: 0.8346 (m-10) cc_final: 0.8102 (m-10) REVERT: C 907 MET cc_start: 0.2010 (ppp) cc_final: 0.1142 (tpt) REVERT: C 966 PHE cc_start: 0.7044 (m-80) cc_final: 0.6587 (m-80) REVERT: C 1002 LYS cc_start: 0.7383 (ttmp) cc_final: 0.6851 (mtmt) REVERT: C 1009 PHE cc_start: 0.7396 (m-80) cc_final: 0.7160 (t80) REVERT: D 36 PHE cc_start: 0.7089 (t80) cc_final: 0.6566 (t80) REVERT: D 133 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: D 189 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7074 (mm-30) REVERT: D 361 MET cc_start: 0.8268 (mtp) cc_final: 0.7834 (mtp) REVERT: D 515 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: D 527 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7091 (mmt) REVERT: D 585 MET cc_start: 0.8764 (mmt) cc_final: 0.8444 (mmt) REVERT: E 81 MET cc_start: 0.8971 (ttt) cc_final: 0.8606 (tmm) REVERT: E 88 TRP cc_start: 0.6446 (m100) cc_final: 0.5686 (t60) REVERT: E 115 VAL cc_start: 0.5804 (OUTLIER) cc_final: 0.5496 (m) REVERT: E 116 MET cc_start: 0.0642 (tpp) cc_final: -0.0001 (pmm) REVERT: E 122 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6005 (mm) REVERT: F 88 TRP cc_start: 0.6451 (m100) cc_final: 0.5611 (t60) REVERT: F 115 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5459 (m) REVERT: F 116 MET cc_start: 0.0470 (tpp) cc_final: -0.0259 (pmm) outliers start: 73 outliers final: 55 residues processed: 401 average time/residue: 0.1772 time to fit residues: 120.3142 Evaluate side-chains 394 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 346 optimal weight: 0.0030 chunk 321 optimal weight: 1.9990 chunk 360 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 337 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 985 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.142452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106410 restraints weight = 54272.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108397 restraints weight = 40335.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108655 restraints weight = 36329.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108952 restraints weight = 24883.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110358 restraints weight = 22567.465| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31823 Z= 0.141 Angle : 0.859 31.489 42940 Z= 0.377 Chirality : 0.084 2.197 4702 Planarity : 0.003 0.038 5286 Dihedral : 11.414 143.921 4630 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.93 % Favored : 88.81 % Rotamer: Outliers : 2.27 % Allowed : 17.72 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.85 (0.14), residues: 3762 helix: 0.43 (0.13), residues: 1804 sheet: -3.23 (0.25), residues: 368 loop : -2.74 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 30 TYR 0.026 0.001 TYR B 702 PHE 0.025 0.001 PHE A 937 TRP 0.018 0.001 TRP E 136 HIS 0.013 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (31813) covalent geometry : angle 0.85818 / 0.38 (42920) SS BOND : bond 0.00357 / 0.19 ( 10) SS BOND : angle 1.64723 / 0.96 ( 20) hydrogen bonds : bond 0.03250 / 2.15 ( 1093) hydrogen bonds : angle 4.12425 / 2.81 ( 3201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 338 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7795 (ptm) cc_final: 0.7582 (ptp) REVERT: A 638 ASP cc_start: 0.8302 (m-30) cc_final: 0.7596 (t0) REVERT: A 642 GLN cc_start: 0.7469 (mp10) cc_final: 0.7160 (mp10) REVERT: A 879 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7919 (mmmt) REVERT: A 891 PHE cc_start: 0.8377 (m-10) cc_final: 0.8085 (m-80) REVERT: A 939 MET cc_start: 0.7418 (tpt) cc_final: 0.6937 (ttm) REVERT: A 966 PHE cc_start: 0.7066 (m-80) cc_final: 0.6451 (m-80) REVERT: A 988 MET cc_start: 0.7954 (tmm) cc_final: 0.7615 (tmm) REVERT: A 1009 PHE cc_start: 0.7684 (t80) cc_final: 0.7465 (t80) REVERT: B 41 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.3873 (p90) REVERT: B 189 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 357 THR cc_start: 0.7937 (p) cc_final: 0.7616 (t) REVERT: B 361 MET cc_start: 0.8229 (mtp) cc_final: 0.7683 (mtp) REVERT: B 404 PRO cc_start: 0.8356 (Cg_exo) cc_final: 0.8108 (Cg_endo) REVERT: B 515 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: B 573 ILE cc_start: 0.8401 (tp) cc_final: 0.8091 (tp) REVERT: B 585 MET cc_start: 0.8808 (mmt) cc_final: 0.8388 (mmt) REVERT: B 814 PHE cc_start: 0.7254 (t80) cc_final: 0.6793 (t80) REVERT: C 414 MET cc_start: 0.7856 (ptm) cc_final: 0.7565 (ptp) REVERT: C 721 MET cc_start: 0.7912 (ptt) cc_final: 0.7699 (ptt) REVERT: C 860 TYR cc_start: 0.7851 (m-80) cc_final: 0.7551 (m-10) REVERT: C 863 TYR cc_start: 0.6262 (m-10) cc_final: 0.5692 (m-10) REVERT: C 891 PHE cc_start: 0.8341 (m-10) cc_final: 0.8099 (m-10) REVERT: C 966 PHE cc_start: 0.6959 (m-80) cc_final: 0.6538 (m-80) REVERT: C 1002 LYS cc_start: 0.7494 (ttmp) cc_final: 0.6952 (mtmt) REVERT: D 36 PHE cc_start: 0.6957 (t80) cc_final: 0.6450 (t80) REVERT: D 133 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: D 189 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7057 (mm-30) REVERT: D 361 MET cc_start: 0.8253 (mtp) cc_final: 0.7809 (mtp) REVERT: D 515 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: D 527 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7090 (mmt) REVERT: D 585 MET cc_start: 0.8782 (mmt) cc_final: 0.8533 (mmt) REVERT: E 81 MET cc_start: 0.9018 (ttt) cc_final: 0.8647 (tmm) REVERT: E 88 TRP cc_start: 0.6441 (m100) cc_final: 0.5689 (t60) REVERT: E 116 MET cc_start: 0.0811 (tpp) cc_final: 0.0216 (pmm) REVERT: E 122 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.5951 (mm) REVERT: F 66 LYS cc_start: 0.7663 (mttt) cc_final: 0.7295 (mttm) REVERT: F 88 TRP cc_start: 0.6394 (m100) cc_final: 0.5581 (t60) REVERT: F 115 VAL cc_start: 0.5650 (OUTLIER) cc_final: 0.5298 (m) REVERT: F 116 MET cc_start: 0.0425 (tpp) cc_final: -0.0271 (pmm) outliers start: 74 outliers final: 57 residues processed: 394 average time/residue: 0.1682 time to fit residues: 113.4217 Evaluate side-chains 386 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 311 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 88 optimal weight: 0.0020 chunk 176 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107115 restraints weight = 54022.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107853 restraints weight = 36459.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108308 restraints weight = 36730.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108725 restraints weight = 25761.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109896 restraints weight = 22914.366| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31823 Z= 0.121 Angle : 0.856 31.333 42940 Z= 0.374 Chirality : 0.083 2.187 4702 Planarity : 0.003 0.038 5286 Dihedral : 11.235 143.091 4630 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.66 % Favored : 89.13 % Rotamer: Outliers : 2.03 % Allowed : 18.18 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.74 (0.14), residues: 3762 helix: 0.55 (0.13), residues: 1806 sheet: -3.18 (0.25), residues: 368 loop : -2.74 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 303 TYR 0.024 0.001 TYR B 702 PHE 0.026 0.001 PHE A 937 TRP 0.018 0.001 TRP E 136 HIS 0.013 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (31813) covalent geometry : angle 0.85546 / 0.37 (42920) SS BOND : bond 0.00234 / 0.12 ( 10) SS BOND : angle 1.65763 / 0.95 ( 20) hydrogen bonds : bond 0.03161 / 2.09 ( 1093) hydrogen bonds : angle 4.06210 / 2.77 ( 3201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 344 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7861 (ptm) cc_final: 0.7604 (ptp) REVERT: A 508 GLN cc_start: 0.5750 (OUTLIER) cc_final: 0.5469 (mm-40) REVERT: A 638 ASP cc_start: 0.8283 (m-30) cc_final: 0.7581 (t0) REVERT: A 642 GLN cc_start: 0.7448 (mp10) cc_final: 0.7123 (mp10) REVERT: A 866 GLU cc_start: 0.7137 (tp30) cc_final: 0.6857 (tm-30) REVERT: A 879 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7604 (mmmt) REVERT: A 891 PHE cc_start: 0.8350 (m-10) cc_final: 0.8096 (m-80) REVERT: A 939 MET cc_start: 0.7449 (tpt) cc_final: 0.6924 (ttm) REVERT: A 966 PHE cc_start: 0.7042 (m-80) cc_final: 0.6406 (m-80) REVERT: A 988 MET cc_start: 0.7923 (tmm) cc_final: 0.7683 (tmm) REVERT: A 1009 PHE cc_start: 0.7738 (t80) cc_final: 0.7511 (t80) REVERT: B 41 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.3873 (p90) REVERT: B 189 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 337 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: B 357 THR cc_start: 0.7874 (p) cc_final: 0.7549 (t) REVERT: B 361 MET cc_start: 0.8221 (mtp) cc_final: 0.7686 (mtp) REVERT: B 404 PRO cc_start: 0.8335 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: B 515 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7785 (m-10) REVERT: B 573 ILE cc_start: 0.8327 (tp) cc_final: 0.8026 (tp) REVERT: B 585 MET cc_start: 0.8744 (mmt) cc_final: 0.8364 (mmt) REVERT: B 814 PHE cc_start: 0.7302 (t80) cc_final: 0.6828 (t80) REVERT: C 414 MET cc_start: 0.7868 (ptm) cc_final: 0.7568 (ptp) REVERT: C 860 TYR cc_start: 0.7916 (m-80) cc_final: 0.7569 (m-10) REVERT: C 863 TYR cc_start: 0.6129 (m-10) cc_final: 0.5562 (m-10) REVERT: C 891 PHE cc_start: 0.8312 (m-10) cc_final: 0.8041 (m-80) REVERT: C 907 MET cc_start: 0.1010 (OUTLIER) cc_final: 0.0542 (tpt) REVERT: C 966 PHE cc_start: 0.7073 (m-80) cc_final: 0.6621 (m-80) REVERT: C 1002 LYS cc_start: 0.7480 (ttmp) cc_final: 0.6958 (mtmt) REVERT: D 133 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: D 189 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7071 (mm-30) REVERT: D 361 MET cc_start: 0.8261 (mtp) cc_final: 0.7840 (mtp) REVERT: D 515 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: D 527 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7070 (mmt) REVERT: D 585 MET cc_start: 0.8761 (mmt) cc_final: 0.8512 (mmt) REVERT: E 81 MET cc_start: 0.9000 (ttt) cc_final: 0.8647 (tmm) REVERT: E 88 TRP cc_start: 0.6473 (m100) cc_final: 0.5740 (t60) REVERT: E 116 MET cc_start: 0.0749 (tpp) cc_final: 0.0060 (pmm) REVERT: E 130 TYR cc_start: 0.4471 (m-80) cc_final: 0.4231 (m-80) REVERT: F 66 LYS cc_start: 0.7626 (mttt) cc_final: 0.7265 (mttm) REVERT: F 88 TRP cc_start: 0.6396 (m100) cc_final: 0.5530 (t60) REVERT: F 115 VAL cc_start: 0.5496 (OUTLIER) cc_final: 0.5099 (m) REVERT: F 116 MET cc_start: 0.0432 (tpp) cc_final: -0.0249 (pmm) outliers start: 66 outliers final: 50 residues processed: 391 average time/residue: 0.1688 time to fit residues: 112.9459 Evaluate side-chains 388 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 227 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 237 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 270 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 412 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105333 restraints weight = 54528.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106905 restraints weight = 39168.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106849 restraints weight = 40349.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107448 restraints weight = 26014.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107699 restraints weight = 23061.193| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31823 Z= 0.178 Angle : 0.874 31.531 42940 Z= 0.386 Chirality : 0.084 2.199 4702 Planarity : 0.004 0.040 5286 Dihedral : 11.221 143.480 4630 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.46 % Favored : 88.38 % Rotamer: Outliers : 2.18 % Allowed : 18.09 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.74 (0.14), residues: 3762 helix: 0.58 (0.13), residues: 1804 sheet: -3.21 (0.25), residues: 370 loop : -2.77 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.031 0.002 TYR F 72 PHE 0.023 0.001 PHE A 937 TRP 0.020 0.001 TRP E 136 HIS 0.014 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (31813) covalent geometry : angle 0.87301 / 0.39 (42920) SS BOND : bond 0.00296 / 0.17 ( 10) SS BOND : angle 1.68071 / 0.97 ( 20) hydrogen bonds : bond 0.03301 / 2.17 ( 1093) hydrogen bonds : angle 4.11936 / 2.81 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.70 seconds wall clock time: 95 minutes 2.46 seconds (5702.46 seconds total)