Starting phenix.real_space_refine on Tue Aug 26 00:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss2_40741/08_2025/8ss2_40741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss2_40741/08_2025/8ss2_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_40741/08_2025/8ss2_40741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss2_40741/08_2025/8ss2_40741.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss2_40741/08_2025/8ss2_40741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss2_40741/08_2025/8ss2_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 263 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: 85 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: 263 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: 85 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: 50 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: 50 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: 7.42, per 1000 atoms: 0.24 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.19 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: 6.68 Time building geometry restraints manager: 3.77 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 - 35.43: 18529 35.43 - 70.86: 553 70.86 - 106.29: 89 106.29 - 141.73: 47 141.73 - 177.16: 21 Dihedral angle restraints: 19239 sinusoidal: 8259 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 19236 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: 4.960 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 18.885 177.158 12189 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 aren 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 covalent geometry : bond 0.02539 (31813) covalent geometry : angle 1.63617 (42920) SS BOND : bond 0.02044 ( 10) SS BOND : angle 3.29454 ( 20) hydrogen bonds : bond 0.29930 ( 1093) hydrogen bonds : angle 10.37714 ( 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 : 1.205 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: 0.8004 (ptm) cc_final: 0.7786 (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: 0.7815 (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: 0.2118 time to fit residues: 234.8652 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 : 1.260 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 60 ASN A 167 ASN A 202 ASN A 344 ASN A 575 ASN A 726 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106488 restraints weight = 54753.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108625 restraints weight = 38088.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108486 restraints weight = 39425.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109491 restraints weight = 25316.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110378 restraints weight = 22217.123| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31823 Z= 0.178 Angle : 0.976 31.976 42940 Z= 0.451 Chirality : 0.090 2.476 4702 Planarity : 0.005 0.059 5286 Dihedral : 19.559 179.461 5190 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.94 % Favored : 87.61 % Rotamer: Outliers : 2.89 % Allowed : 11.15 % Favored : 85.96 % 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 aren not related in a simple way. whole: -4.15 (0.12), residues: 3762 helix: -1.95 (0.11), residues: 1770 sheet: -4.10 (0.23), residues: 370 loop : -3.28 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 692 TYR 0.030 0.002 TYR C1001 PHE 0.029 0.002 PHE C 517 TRP 0.016 0.001 TRP D 766 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00393 (31813) covalent geometry : angle 0.97441 (42920) SS BOND : bond 0.00652 ( 10) SS BOND : angle 2.73983 ( 20) hydrogen bonds : bond 0.05309 ( 1093) hydrogen bonds : angle 5.36270 ( 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: 94 poor density : 477 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8841 (pt) cc_final: 0.8610 (pt) REVERT: A 186 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8611 (pp) REVERT: A 302 GLN cc_start: 0.7628 (pm20) cc_final: 0.7342 (mp10) REVERT: A 414 MET cc_start: 0.7796 (ptm) cc_final: 0.7556 (ptp) REVERT: A 463 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: A 638 ASP cc_start: 0.8375 (m-30) cc_final: 0.8055 (m-30) REVERT: A 879 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7902 (mmmt) REVERT: A 891 PHE cc_start: 0.8470 (m-10) cc_final: 0.8079 (m-10) REVERT: A 901 PHE cc_start: 0.6858 (m-80) cc_final: 0.6432 (m-10) REVERT: A 939 MET cc_start: 0.7739 (ttm) cc_final: 0.7464 (tpt) REVERT: A 966 PHE cc_start: 0.6938 (m-80) cc_final: 0.6476 (m-80) REVERT: A 985 ASN cc_start: 0.7354 (m110) cc_final: 0.7032 (m110) REVERT: A 1005 TRP cc_start: 0.7202 (p-90) cc_final: 0.6881 (p-90) REVERT: B 46 HIS cc_start: 0.7388 (t-90) cc_final: 0.7012 (t-170) REVERT: B 133 PHE cc_start: 0.8851 (m-10) cc_final: 0.8477 (m-10) REVERT: B 189 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 357 THR cc_start: 0.7987 (p) cc_final: 0.7586 (t) REVERT: B 361 MET cc_start: 0.8192 (mtp) cc_final: 0.7633 (mtp) REVERT: B 392 GLN cc_start: 0.7669 (mp10) cc_final: 0.7304 (mp10) REVERT: B 527 MET cc_start: 0.7684 (tpp) cc_final: 0.7409 (mmt) REVERT: B 573 ILE cc_start: 0.8754 (tp) cc_final: 0.8495 (tp) REVERT: C 50 LEU cc_start: 0.8681 (pt) cc_final: 0.8374 (pt) REVERT: C 302 GLN cc_start: 0.7607 (pm20) cc_final: 0.7294 (mp10) REVERT: C 412 HIS cc_start: 0.7351 (t-170) cc_final: 0.7050 (t70) REVERT: C 414 MET cc_start: 0.7808 (ptm) cc_final: 0.7571 (ptp) REVERT: C 545 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.7159 (ttt180) REVERT: C 627 GLU cc_start: 0.8186 (pp20) cc_final: 0.7687 (tm-30) REVERT: C 635 SER cc_start: 0.8978 (t) cc_final: 0.8745 (p) REVERT: C 670 MET cc_start: 0.9186 (mtm) cc_final: 0.8969 (mtp) REVERT: C 816 TYR cc_start: 0.7817 (t80) cc_final: 0.7481 (t80) REVERT: C 863 TYR cc_start: 0.5962 (m-10) cc_final: 0.5320 (m-10) REVERT: C 891 PHE cc_start: 0.8319 (m-10) cc_final: 0.8040 (m-80) REVERT: C 907 MET cc_start: 0.2065 (ppp) cc_final: 0.1476 (tpt) REVERT: C 966 PHE cc_start: 0.7051 (m-80) cc_final: 0.6434 (m-80) REVERT: D 33 MET cc_start: 0.8719 (ptm) cc_final: 0.8476 (ptt) REVERT: D 269 GLU cc_start: 0.7618 (tp30) cc_final: 0.7094 (tp30) REVERT: D 357 THR cc_start: 0.7751 (p) cc_final: 0.7503 (t) REVERT: D 392 GLN cc_start: 0.7483 (mp10) cc_final: 0.7067 (mp10) REVERT: D 408 MET cc_start: 0.7176 (mmm) cc_final: 0.5346 (mmm) REVERT: D 585 MET cc_start: 0.8804 (mmt) cc_final: 0.8094 (mmm) REVERT: D 773 CYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7503 (m) REVERT: E 88 TRP cc_start: 0.6547 (m100) cc_final: 0.5495 (t60) REVERT: E 116 MET cc_start: 0.1262 (tpp) cc_final: 0.0070 (pmm) REVERT: F 88 TRP cc_start: 0.6459 (m100) cc_final: 0.5523 (t60) REVERT: F 116 MET cc_start: 0.0707 (tpp) cc_final: 0.0056 (pmm) outliers start: 94 outliers final: 32 residues processed: 540 average time/residue: 0.1900 time to fit residues: 170.9760 Evaluate side-chains 411 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 358 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 ILE 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 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: 9.9990 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 311 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 167 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 E 129 ASN F 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106519 restraints weight = 54729.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106928 restraints weight = 38719.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107877 restraints weight = 36645.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108211 restraints weight = 26498.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109195 restraints weight = 23895.186| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 31823 Z= 0.149 Angle : 0.907 32.883 42940 Z= 0.410 Chirality : 0.083 2.267 4702 Planarity : 0.004 0.052 5286 Dihedral : 18.658 177.899 5186 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.30 % Favored : 88.33 % Rotamer: Outliers : 2.70 % Allowed : 13.24 % Favored : 84.06 % 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 aren not related in a simple way. whole: -3.27 (0.13), residues: 3762 helix: -1.02 (0.12), residues: 1778 sheet: -3.92 (0.23), residues: 362 loop : -3.04 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 545 TYR 0.025 0.002 TYR C1001 PHE 0.021 0.001 PHE A 347 TRP 0.015 0.001 TRP A 887 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00332 (31813) covalent geometry : angle 0.90542 (42920) SS BOND : bond 0.00999 ( 10) SS BOND : angle 2.32002 ( 20) hydrogen bonds : bond 0.04213 ( 1093) hydrogen bonds : angle 4.70517 ( 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 510 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 422 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7573 (ptm160) REVERT: A 50 LEU cc_start: 0.8759 (pt) cc_final: 0.8528 (pt) REVERT: A 414 MET cc_start: 0.7762 (ptm) cc_final: 0.7554 (ptp) REVERT: A 638 ASP cc_start: 0.8281 (m-30) cc_final: 0.7881 (t0) REVERT: A 879 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7917 (mmmt) REVERT: A 891 PHE cc_start: 0.8464 (m-10) cc_final: 0.8220 (m-80) REVERT: A 901 PHE cc_start: 0.6810 (m-80) cc_final: 0.6373 (m-10) REVERT: A 907 MET cc_start: 0.2126 (OUTLIER) cc_final: 0.1186 (tpt) REVERT: A 924 MET cc_start: 0.7361 (pmm) cc_final: 0.7091 (pmm) REVERT: A 939 MET cc_start: 0.7595 (ttm) cc_final: 0.7281 (tpt) REVERT: A 966 PHE cc_start: 0.6919 (m-80) cc_final: 0.6455 (m-80) REVERT: A 988 MET cc_start: 0.8186 (tmm) cc_final: 0.7581 (tmm) REVERT: A 1005 TRP cc_start: 0.7224 (p-90) cc_final: 0.6920 (p-90) REVERT: B 33 MET cc_start: 0.8669 (ptm) cc_final: 0.8354 (ptt) REVERT: B 74 PHE cc_start: 0.8110 (t80) cc_final: 0.7825 (t80) REVERT: B 133 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (m-10) REVERT: B 189 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 357 THR cc_start: 0.7966 (p) cc_final: 0.7610 (t) REVERT: B 361 MET cc_start: 0.8165 (mtp) cc_final: 0.7860 (mtp) REVERT: B 392 GLN cc_start: 0.7720 (mp10) cc_final: 0.7357 (mp10) REVERT: B 408 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.5882 (mmm) REVERT: B 527 MET cc_start: 0.7637 (tpp) cc_final: 0.7284 (mmt) REVERT: B 573 ILE cc_start: 0.8663 (tp) cc_final: 0.8412 (tp) REVERT: C 42 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7717 (ptm160) REVERT: C 50 LEU cc_start: 0.8600 (pt) cc_final: 0.8298 (pt) REVERT: C 414 MET cc_start: 0.7858 (ptm) cc_final: 0.7509 (ptp) REVERT: C 585 MET cc_start: 0.8104 (mpt) cc_final: 0.7839 (mpt) REVERT: C 627 GLU cc_start: 0.8096 (pp20) cc_final: 0.7782 (tm-30) REVERT: C 635 SER cc_start: 0.9036 (t) cc_final: 0.8806 (p) REVERT: C 816 TYR cc_start: 0.7793 (t80) cc_final: 0.7490 (t80) REVERT: C 863 TYR cc_start: 0.5977 (m-10) cc_final: 0.5256 (m-10) REVERT: C 891 PHE cc_start: 0.8379 (m-10) cc_final: 0.8098 (m-80) REVERT: C 907 MET cc_start: 0.2202 (ppp) cc_final: 0.1439 (tpt) REVERT: C 924 MET cc_start: 0.7322 (ptp) cc_final: 0.6807 (mtm) REVERT: C 966 PHE cc_start: 0.7099 (m-80) cc_final: 0.6466 (m-80) REVERT: C 985 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7007 (p0) REVERT: C 1002 LYS cc_start: 0.7276 (ttmp) cc_final: 0.6682 (mtmt) REVERT: C 1025 VAL cc_start: 0.8137 (t) cc_final: 0.7934 (p) REVERT: D 33 MET cc_start: 0.8587 (ptm) cc_final: 0.8343 (ptt) REVERT: D 189 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7282 (mm-30) REVERT: D 361 MET cc_start: 0.8131 (mtp) cc_final: 0.7852 (mtp) REVERT: D 373 TYR cc_start: 0.8937 (p90) cc_final: 0.8604 (p90) REVERT: D 392 GLN cc_start: 0.7462 (mp10) cc_final: 0.7147 (mp10) REVERT: D 585 MET cc_start: 0.8730 (mmt) cc_final: 0.7909 (mmt) REVERT: E 81 MET cc_start: 0.8743 (ttt) cc_final: 0.8538 (tmm) REVERT: E 88 TRP cc_start: 0.6598 (m100) cc_final: 0.5616 (t60) REVERT: E 115 VAL cc_start: 0.6847 (OUTLIER) cc_final: 0.6439 (m) REVERT: E 116 MET cc_start: 0.0998 (tpp) cc_final: 0.0453 (pmm) REVERT: E 122 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6680 (mm) REVERT: F 10 TYR cc_start: 0.8180 (m-80) cc_final: 0.7599 (m-10) REVERT: F 88 TRP cc_start: 0.6504 (m100) cc_final: 0.5602 (t60) REVERT: F 116 MET cc_start: 0.0895 (tpp) cc_final: 0.0071 (pmm) outliers start: 88 outliers final: 45 residues processed: 484 average time/residue: 0.1909 time to fit residues: 153.6812 Evaluate side-chains 411 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 358 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 635 SER 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 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 396 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 604 VAL 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 233 LEU Chi-restraints excluded: chain C residue 335 GLN 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 274 HIS Chi-restraints excluded: chain D residue 299 LEU 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 D residue 789 LEU 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 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 135 optimal weight: 0.0030 chunk 296 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 316 optimal weight: 9.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 246 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104032 restraints weight = 54586.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103652 restraints weight = 36814.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104345 restraints weight = 38569.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104675 restraints weight = 27764.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105011 restraints weight = 24809.577| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31823 Z= 0.191 Angle : 0.902 32.986 42940 Z= 0.407 Chirality : 0.083 2.237 4702 Planarity : 0.004 0.057 5286 Dihedral : 18.158 178.908 5184 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.91 % Favored : 87.72 % Rotamer: Outliers : 2.95 % Allowed : 14.07 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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 aren not related in a simple way. whole: -2.87 (0.13), residues: 3762 helix: -0.58 (0.12), residues: 1768 sheet: -3.81 (0.23), residues: 386 loop : -2.93 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.026 0.002 TYR C1001 PHE 0.021 0.002 PHE A 937 TRP 0.015 0.001 TRP A 262 HIS 0.009 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00442 (31813) covalent geometry : angle 0.90148 (42920) SS BOND : bond 0.00367 ( 10) SS BOND : angle 1.81523 ( 20) hydrogen bonds : bond 0.03889 ( 1093) hydrogen bonds : angle 4.53294 ( 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 475 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 379 time to evaluate : 1.293 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: 0.8765 (pt) cc_final: 0.8506 (pt) REVERT: A 408 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7216 (mpp) REVERT: A 414 MET cc_start: 0.7780 (ptm) cc_final: 0.7539 (ptp) REVERT: A 642 GLN cc_start: 0.7534 (mp10) cc_final: 0.7258 (mp10) REVERT: A 879 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7921 (mmmt) REVERT: A 891 PHE cc_start: 0.8459 (m-10) cc_final: 0.8177 (m-80) REVERT: A 907 MET cc_start: 0.1893 (OUTLIER) cc_final: 0.1024 (tpt) REVERT: A 939 MET cc_start: 0.7652 (ttm) cc_final: 0.7341 (tpt) REVERT: A 966 PHE cc_start: 0.6970 (m-80) cc_final: 0.6570 (m-80) REVERT: A 988 MET cc_start: 0.8273 (tmm) cc_final: 0.7522 (tmm) REVERT: A 1005 TRP cc_start: 0.7230 (p-90) cc_final: 0.6907 (p-90) REVERT: A 1029 MET cc_start: 0.7570 (mmt) cc_final: 0.7211 (tpp) REVERT: B 357 THR cc_start: 0.8070 (p) cc_final: 0.7716 (t) REVERT: B 361 MET cc_start: 0.8296 (mtp) cc_final: 0.7978 (mtp) REVERT: B 392 GLN cc_start: 0.7759 (mp10) cc_final: 0.7402 (mp10) REVERT: B 408 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.5734 (mmm) REVERT: B 527 MET cc_start: 0.7683 (tpp) cc_final: 0.7309 (mmt) REVERT: B 573 ILE cc_start: 0.8593 (tp) cc_final: 0.8329 (tp) REVERT: B 814 PHE cc_start: 0.7163 (t80) cc_final: 0.6923 (t80) REVERT: C 50 LEU cc_start: 0.8632 (pt) cc_final: 0.8304 (pt) REVERT: C 262 TRP cc_start: 0.8376 (t-100) cc_final: 0.8113 (t-100) REVERT: C 414 MET cc_start: 0.7952 (ptm) cc_final: 0.7580 (ptp) REVERT: C 627 GLU cc_start: 0.8206 (pp20) cc_final: 0.7950 (tm-30) REVERT: C 721 MET cc_start: 0.8124 (ptt) cc_final: 0.7842 (ptt) REVERT: C 816 TYR cc_start: 0.7781 (t80) cc_final: 0.7479 (t80) REVERT: C 863 TYR cc_start: 0.6047 (m-10) cc_final: 0.5371 (m-10) REVERT: C 891 PHE cc_start: 0.8384 (m-10) cc_final: 0.8082 (m-80) REVERT: C 907 MET cc_start: 0.1919 (ppp) cc_final: 0.1096 (tpt) REVERT: C 924 MET cc_start: 0.7420 (ptp) cc_final: 0.6877 (mtm) REVERT: C 966 PHE cc_start: 0.6995 (m-80) cc_final: 0.6360 (m-80) REVERT: C 985 ASN cc_start: 0.7724 (p0) cc_final: 0.6817 (p0) REVERT: C 1002 LYS cc_start: 0.7258 (ttmp) cc_final: 0.6688 (mtmt) REVERT: C 1009 PHE cc_start: 0.7473 (m-80) cc_final: 0.7098 (t80) REVERT: D 133 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8706 (m-10) REVERT: D 189 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 248 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7431 (t) REVERT: D 361 MET cc_start: 0.8284 (mtp) cc_final: 0.8002 (mtp) REVERT: D 515 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: D 527 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.6989 (mmt) REVERT: D 585 MET cc_start: 0.8850 (mmt) cc_final: 0.8378 (mmm) REVERT: E 81 MET cc_start: 0.8911 (ttt) cc_final: 0.8584 (tmm) REVERT: E 88 TRP cc_start: 0.6646 (m100) cc_final: 0.5643 (t60) REVERT: E 116 MET cc_start: 0.1052 (tpp) cc_final: -0.0025 (pmm) REVERT: E 122 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6317 (mm) REVERT: F 88 TRP cc_start: 0.6609 (m100) cc_final: 0.5621 (t60) REVERT: F 116 MET cc_start: 0.0615 (tpp) cc_final: -0.0242 (pmm) outliers start: 96 outliers final: 60 residues processed: 445 average time/residue: 0.1917 time to fit residues: 141.7826 Evaluate side-chains 413 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 408 MET 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 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 591 ILE 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 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 633 ILE Chi-restraints excluded: chain D residue 683 VAL 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 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 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: 0.7980 chunk 196 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 24 GLN ** 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 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105667 restraints weight = 54666.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104937 restraints weight = 38074.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105839 restraints weight = 34703.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107527 restraints weight = 26158.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107711 restraints weight = 22952.566| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3873 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= 0.129 Angle : 0.863 32.897 42940 Z= 0.382 Chirality : 0.081 2.205 4702 Planarity : 0.004 0.043 5286 Dihedral : 17.728 178.725 5184 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.24 % Favored : 88.49 % Rotamer: Outliers : 2.27 % Allowed : 15.82 % Favored : 81.91 % 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 aren not related in a simple way. whole: -2.50 (0.14), residues: 3762 helix: -0.22 (0.12), residues: 1776 sheet: -3.70 (0.23), residues: 384 loop : -2.80 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.026 0.001 TYR C1001 PHE 0.019 0.001 PHE D 515 TRP 0.014 0.001 TRP A 262 HIS 0.008 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00290 (31813) covalent geometry : angle 0.86267 (42920) SS BOND : bond 0.00211 ( 10) SS BOND : angle 1.56146 ( 20) hydrogen bonds : bond 0.03533 ( 1093) hydrogen bonds : angle 4.30141 ( 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 463 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 389 time to evaluate : 1.238 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: 0.8539 (pt) cc_final: 0.8273 (pt) REVERT: A 262 TRP cc_start: 0.8476 (t-100) cc_final: 0.8083 (t-100) REVERT: A 408 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: A 414 MET cc_start: 0.7749 (ptm) cc_final: 0.7525 (ptp) REVERT: A 642 GLN cc_start: 0.7521 (mp10) cc_final: 0.7183 (mp10) REVERT: A 879 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7882 (mmmt) REVERT: A 891 PHE cc_start: 0.8445 (m-10) cc_final: 0.8179 (m-80) REVERT: A 966 PHE cc_start: 0.6959 (m-80) cc_final: 0.6548 (m-80) REVERT: A 988 MET cc_start: 0.8193 (tmm) cc_final: 0.7882 (tmm) REVERT: A 1005 TRP cc_start: 0.7189 (p-90) cc_final: 0.6978 (p-90) REVERT: B 189 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7178 (mm-30) REVERT: B 357 THR cc_start: 0.7951 (p) cc_final: 0.7601 (t) REVERT: B 361 MET cc_start: 0.8253 (mtp) cc_final: 0.7963 (mtp) REVERT: B 392 GLN cc_start: 0.7661 (mp10) cc_final: 0.7375 (mp10) REVERT: B 408 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.5988 (mmt) REVERT: B 412 HIS cc_start: 0.6783 (t-170) cc_final: 0.6534 (t-170) REVERT: B 425 CYS cc_start: 0.7287 (m) cc_final: 0.6930 (m) REVERT: B 573 ILE cc_start: 0.8458 (tp) cc_final: 0.8195 (tp) REVERT: B 585 MET cc_start: 0.8794 (mmt) cc_final: 0.8074 (mmt) REVERT: B 814 PHE cc_start: 0.7227 (t80) cc_final: 0.6963 (t80) REVERT: C 189 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8023 (tp30) REVERT: C 414 MET cc_start: 0.7899 (ptm) cc_final: 0.7550 (ptp) REVERT: C 721 MET cc_start: 0.8034 (ptt) cc_final: 0.7804 (ptt) REVERT: C 816 TYR cc_start: 0.7776 (t80) cc_final: 0.7503 (t80) REVERT: C 863 TYR cc_start: 0.6082 (m-10) cc_final: 0.5477 (m-10) REVERT: C 891 PHE cc_start: 0.8389 (m-10) cc_final: 0.8117 (m-10) REVERT: C 907 MET cc_start: 0.2046 (ppp) cc_final: 0.1106 (tpt) REVERT: C 966 PHE cc_start: 0.7095 (m-80) cc_final: 0.6508 (m-80) REVERT: C 985 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7005 (p0) REVERT: C 1002 LYS cc_start: 0.7298 (ttmp) cc_final: 0.6714 (mtmt) REVERT: C 1009 PHE cc_start: 0.7456 (m-80) cc_final: 0.7111 (t80) REVERT: D 36 PHE cc_start: 0.7097 (t80) cc_final: 0.6562 (t80) REVERT: D 189 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 248 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (t) REVERT: D 361 MET cc_start: 0.8257 (mtp) cc_final: 0.7891 (mtp) REVERT: D 498 LEU cc_start: 0.9048 (pt) cc_final: 0.8560 (pt) REVERT: D 515 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: D 527 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7083 (mmt) REVERT: D 585 MET cc_start: 0.8795 (mmt) cc_final: 0.8253 (mmt) REVERT: E 81 MET cc_start: 0.8917 (ttt) cc_final: 0.8595 (tmm) REVERT: E 88 TRP cc_start: 0.6615 (m100) cc_final: 0.5685 (t60) REVERT: E 116 MET cc_start: 0.1108 (tpp) cc_final: 0.0166 (pmm) REVERT: E 122 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6380 (mm) REVERT: F 88 TRP cc_start: 0.6476 (m100) cc_final: 0.5473 (t60) REVERT: F 115 VAL cc_start: 0.6286 (OUTLIER) cc_final: 0.5954 (m) REVERT: F 116 MET cc_start: 0.0937 (tpp) cc_final: -0.0155 (pmm) outliers start: 74 outliers final: 50 residues processed: 433 average time/residue: 0.1891 time to fit residues: 137.5016 Evaluate side-chains 402 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 408 MET 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 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 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 700 TYR 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 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 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 95 ILE 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 95 ILE Chi-restraints excluded: chain F residue 115 VAL 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: 1.9990 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 318 optimal weight: 0.0170 chunk 33 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 310 optimal weight: 0.0370 chunk 247 optimal weight: 0.7980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** 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 = 0.3967 r_free = 0.3967 target = 0.143469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107217 restraints weight = 54474.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107246 restraints weight = 35297.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107865 restraints weight = 37349.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108146 restraints weight = 26314.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108472 restraints weight = 23571.288| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31823 Z= 0.126 Angle : 0.858 32.829 42940 Z= 0.379 Chirality : 0.081 2.182 4702 Planarity : 0.003 0.037 5286 Dihedral : 17.440 178.768 5184 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.95 % Favored : 88.76 % Rotamer: Outliers : 2.73 % Allowed : 16.37 % Favored : 80.90 % 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 aren not related in a simple way. whole: -2.24 (0.14), residues: 3762 helix: 0.03 (0.13), residues: 1774 sheet: -3.58 (0.24), residues: 384 loop : -2.72 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.025 0.001 TYR C1001 PHE 0.030 0.001 PHE D 517 TRP 0.021 0.001 TRP C 262 HIS 0.011 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00285 (31813) covalent geometry : angle 0.85794 (42920) SS BOND : bond 0.00177 ( 10) SS BOND : angle 1.40935 ( 20) hydrogen bonds : bond 0.03386 ( 1093) hydrogen bonds : angle 4.18745 ( 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 456 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8437 (pt) cc_final: 0.8144 (pt) REVERT: A 262 TRP cc_start: 0.8460 (t-100) cc_final: 0.8067 (t-100) REVERT: A 408 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7165 (mpp) REVERT: A 414 MET cc_start: 0.7738 (ptm) cc_final: 0.7518 (ptp) REVERT: A 642 GLN cc_start: 0.7545 (mp10) cc_final: 0.7170 (mp10) REVERT: A 879 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7878 (mmmt) REVERT: A 891 PHE cc_start: 0.8444 (m-10) cc_final: 0.8184 (m-80) REVERT: A 939 MET cc_start: 0.7557 (tpt) cc_final: 0.7071 (ttt) REVERT: A 966 PHE cc_start: 0.7064 (m-80) cc_final: 0.6393 (m-80) REVERT: A 988 MET cc_start: 0.8117 (tmm) cc_final: 0.7771 (tmm) REVERT: A 1009 PHE cc_start: 0.7784 (m-80) cc_final: 0.7481 (t80) REVERT: B 357 THR cc_start: 0.7920 (p) cc_final: 0.7552 (t) REVERT: B 361 MET cc_start: 0.8265 (mtp) cc_final: 0.7717 (mtp) REVERT: B 404 PRO cc_start: 0.7891 (Cg_exo) cc_final: 0.7595 (Cg_endo) REVERT: B 408 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6103 (mmt) REVERT: B 425 CYS cc_start: 0.7142 (m) cc_final: 0.6932 (m) REVERT: B 573 ILE cc_start: 0.8358 (tp) cc_final: 0.8094 (tp) REVERT: B 585 MET cc_start: 0.8834 (mmt) cc_final: 0.8129 (mmt) REVERT: B 695 LYS cc_start: 0.7843 (pttp) cc_final: 0.7613 (pttp) REVERT: B 814 PHE cc_start: 0.7249 (t80) cc_final: 0.6812 (t80) REVERT: C 189 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8048 (tp30) REVERT: C 414 MET cc_start: 0.7894 (ptm) cc_final: 0.7552 (ptp) REVERT: C 638 ASP cc_start: 0.8324 (m-30) cc_final: 0.7569 (t0) REVERT: C 721 MET cc_start: 0.7980 (ptt) cc_final: 0.7733 (ptt) REVERT: C 816 TYR cc_start: 0.7802 (t80) cc_final: 0.7354 (t80) REVERT: C 863 TYR cc_start: 0.6069 (m-10) cc_final: 0.5426 (m-10) REVERT: C 891 PHE cc_start: 0.8360 (m-10) cc_final: 0.7995 (m-80) REVERT: C 907 MET cc_start: 0.2084 (ppp) cc_final: 0.1098 (tpt) REVERT: C 924 MET cc_start: 0.7604 (ptp) cc_final: 0.7022 (mtm) REVERT: C 966 PHE cc_start: 0.7075 (m-80) cc_final: 0.6400 (m-80) REVERT: C 1002 LYS cc_start: 0.7372 (ttmp) cc_final: 0.6790 (mtmt) REVERT: C 1009 PHE cc_start: 0.7393 (m-80) cc_final: 0.7108 (t80) REVERT: D 36 PHE cc_start: 0.7093 (t80) cc_final: 0.6615 (t80) REVERT: D 189 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6996 (mm-30) REVERT: D 248 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7294 (t) REVERT: D 314 ASP cc_start: 0.7237 (t0) cc_final: 0.6696 (p0) REVERT: D 361 MET cc_start: 0.8276 (mtp) cc_final: 0.7896 (mtp) REVERT: D 515 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7954 (m-10) REVERT: D 527 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7061 (mmt) REVERT: D 585 MET cc_start: 0.8786 (mmt) cc_final: 0.8292 (mmt) REVERT: E 81 MET cc_start: 0.8905 (ttt) cc_final: 0.8567 (tmm) REVERT: E 88 TRP cc_start: 0.6601 (m100) cc_final: 0.5735 (t60) REVERT: E 116 MET cc_start: 0.1014 (tpp) cc_final: 0.0141 (pmm) REVERT: E 122 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6181 (mm) REVERT: F 10 TYR cc_start: 0.8083 (m-10) cc_final: 0.7825 (m-10) REVERT: F 88 TRP cc_start: 0.6474 (m100) cc_final: 0.5516 (t60) REVERT: F 115 VAL cc_start: 0.6128 (OUTLIER) cc_final: 0.5831 (m) REVERT: F 116 MET cc_start: 0.0699 (tpp) cc_final: -0.0115 (pmm) outliers start: 89 outliers final: 54 residues processed: 430 average time/residue: 0.1940 time to fit residues: 138.6350 Evaluate side-chains 399 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 408 MET 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 744 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 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 408 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 C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 182 GLN 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 626 VAL Chi-restraints excluded: chain C residue 700 TYR Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 354 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 264 optimal weight: 40.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 202 ASN ** C 569 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 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 = 0.3922 r_free = 0.3922 target = 0.140214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103864 restraints weight = 53214.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104595 restraints weight = 36005.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104873 restraints weight = 37602.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106423 restraints weight = 24814.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107278 restraints weight = 20906.433| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31823 Z= 0.182 Angle : 0.881 33.154 42940 Z= 0.391 Chirality : 0.082 2.189 4702 Planarity : 0.004 0.036 5286 Dihedral : 17.218 178.937 5184 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.59 % Favored : 88.14 % Rotamer: Outliers : 2.64 % Allowed : 16.40 % Favored : 80.96 % 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 aren not related in a simple way. whole: -2.17 (0.14), residues: 3762 helix: 0.11 (0.13), residues: 1788 sheet: -3.46 (0.25), residues: 358 loop : -2.77 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 888 TYR 0.026 0.002 TYR C1001 PHE 0.027 0.002 PHE D 517 TRP 0.019 0.001 TRP C 262 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00426 (31813) covalent geometry : angle 0.88022 (42920) SS BOND : bond 0.00285 ( 10) SS BOND : angle 1.58605 ( 20) hydrogen bonds : bond 0.03484 ( 1093) hydrogen bonds : angle 4.24243 ( 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 445 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 359 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8504 (pt) cc_final: 0.8182 (pt) REVERT: A 408 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7132 (mpp) REVERT: A 414 MET cc_start: 0.7695 (ptm) cc_final: 0.7491 (ptp) REVERT: A 642 GLN cc_start: 0.7582 (mp10) cc_final: 0.7146 (mp10) REVERT: A 678 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 879 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7925 (mmmt) REVERT: A 891 PHE cc_start: 0.8439 (m-10) cc_final: 0.8139 (m-80) REVERT: A 939 MET cc_start: 0.7397 (tpt) cc_final: 0.6959 (ttt) REVERT: A 966 PHE cc_start: 0.7028 (m-80) cc_final: 0.6387 (m-80) REVERT: A 988 MET cc_start: 0.8097 (tmm) cc_final: 0.7727 (tmm) REVERT: B 41 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.3778 (p90) REVERT: B 357 THR cc_start: 0.7971 (p) cc_final: 0.7614 (t) REVERT: B 361 MET cc_start: 0.8291 (mtp) cc_final: 0.7729 (mtp) REVERT: B 496 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (ttp) REVERT: B 573 ILE cc_start: 0.8398 (tp) cc_final: 0.8088 (tp) REVERT: B 814 PHE cc_start: 0.7281 (t80) cc_final: 0.6847 (t80) REVERT: C 50 LEU cc_start: 0.8407 (pt) cc_final: 0.8038 (pt) REVERT: C 414 MET cc_start: 0.7886 (ptm) cc_final: 0.7577 (ptp) REVERT: C 721 MET cc_start: 0.8025 (ptt) cc_final: 0.7811 (ptt) REVERT: C 816 TYR cc_start: 0.7775 (t80) cc_final: 0.7342 (t80) REVERT: C 863 TYR cc_start: 0.6192 (m-10) cc_final: 0.5576 (m-10) REVERT: C 891 PHE cc_start: 0.8382 (m-10) cc_final: 0.8142 (m-10) REVERT: C 907 MET cc_start: 0.2143 (ppp) cc_final: 0.1216 (tpt) REVERT: C 1002 LYS cc_start: 0.7453 (ttmp) cc_final: 0.6869 (mtmt) REVERT: C 1009 PHE cc_start: 0.7356 (m-80) cc_final: 0.7108 (t80) REVERT: D 36 PHE cc_start: 0.6921 (t80) cc_final: 0.6458 (t80) REVERT: D 189 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6893 (mm-30) REVERT: D 248 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7443 (m) REVERT: D 361 MET cc_start: 0.8308 (mtp) cc_final: 0.7874 (mtp) REVERT: D 498 LEU cc_start: 0.9076 (pt) cc_final: 0.8698 (pt) REVERT: D 515 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: D 527 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7138 (mmt) REVERT: D 585 MET cc_start: 0.8863 (mmt) cc_final: 0.8499 (mmt) REVERT: E 81 MET cc_start: 0.9019 (ttt) cc_final: 0.8634 (tmm) REVERT: E 88 TRP cc_start: 0.6526 (m100) cc_final: 0.5692 (t60) REVERT: E 116 MET cc_start: 0.0806 (tpp) cc_final: -0.0058 (pmm) REVERT: E 122 ILE cc_start: 0.6540 (mp) cc_final: 0.6060 (mm) REVERT: F 88 TRP cc_start: 0.6418 (m100) cc_final: 0.5619 (t60) REVERT: F 115 VAL cc_start: 0.5849 (OUTLIER) cc_final: 0.5609 (m) REVERT: F 116 MET cc_start: 0.0707 (tpp) cc_final: -0.0103 (pmm) outliers start: 86 outliers final: 63 residues processed: 418 average time/residue: 0.1855 time to fit residues: 130.8297 Evaluate side-chains 400 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 330 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 408 MET 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 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 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 196 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 496 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 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 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 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 C residue 1015 LEU Chi-restraints excluded: chain D residue 196 CYS 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 633 ILE 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 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 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: 4.9990 chunk 313 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 172 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** 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 = 0.143612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106779 restraints weight = 54156.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107109 restraints weight = 35751.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107469 restraints weight = 37297.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108413 restraints weight = 25767.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109570 restraints weight = 22839.416| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.037 31823 Z= 0.117 Angle : 0.858 32.910 42940 Z= 0.375 Chirality : 0.081 2.170 4702 Planarity : 0.003 0.036 5286 Dihedral : 16.899 178.923 5184 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.34 % Favored : 89.45 % Rotamer: Outliers : 2.18 % Allowed : 17.14 % Favored : 80.68 % 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 aren not related in a simple way. whole: -1.96 (0.14), residues: 3762 helix: 0.32 (0.13), residues: 1794 sheet: -3.18 (0.25), residues: 354 loop : -2.78 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 899 TYR 0.024 0.001 TYR C1001 PHE 0.025 0.001 PHE D 517 TRP 0.020 0.001 TRP C 262 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00261 (31813) covalent geometry : angle 0.85778 (42920) SS BOND : bond 0.00397 ( 10) SS BOND : angle 1.57814 ( 20) hydrogen bonds : bond 0.03222 ( 1093) hydrogen bonds : angle 4.14387 ( 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 433 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8243 (pt) cc_final: 0.7925 (pt) REVERT: A 262 TRP cc_start: 0.8498 (t-100) cc_final: 0.8181 (t-100) REVERT: A 408 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: A 414 MET cc_start: 0.7728 (ptm) cc_final: 0.7512 (ptp) REVERT: A 642 GLN cc_start: 0.7515 (mp10) cc_final: 0.7070 (mp10) REVERT: A 678 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 879 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7868 (mmmt) REVERT: A 891 PHE cc_start: 0.8381 (m-10) cc_final: 0.8115 (m-80) REVERT: A 939 MET cc_start: 0.7420 (tpt) cc_final: 0.6893 (ttm) REVERT: A 966 PHE cc_start: 0.7024 (m-80) cc_final: 0.6383 (m-80) REVERT: A 988 MET cc_start: 0.8008 (tmm) cc_final: 0.7636 (tmm) REVERT: A 1009 PHE cc_start: 0.7811 (t80) cc_final: 0.7591 (t80) REVERT: B 41 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.3739 (p90) REVERT: B 189 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6903 (mm-30) REVERT: B 357 THR cc_start: 0.7927 (p) cc_final: 0.7574 (t) REVERT: B 361 MET cc_start: 0.8277 (mtp) cc_final: 0.7726 (mtp) REVERT: B 408 MET cc_start: 0.6699 (mmm) cc_final: 0.6459 (mmp) REVERT: B 496 MET cc_start: 0.8837 (ttp) cc_final: 0.8632 (ttm) REVERT: B 573 ILE cc_start: 0.8259 (tp) cc_final: 0.7963 (tp) REVERT: B 585 MET cc_start: 0.8722 (mmt) cc_final: 0.8323 (mmm) REVERT: B 814 PHE cc_start: 0.7286 (t80) cc_final: 0.6823 (t80) REVERT: C 414 MET cc_start: 0.7873 (ptm) cc_final: 0.7565 (ptp) REVERT: C 721 MET cc_start: 0.7938 (ptt) cc_final: 0.7722 (ptt) REVERT: C 816 TYR cc_start: 0.7680 (t80) cc_final: 0.7257 (t80) REVERT: C 860 TYR cc_start: 0.7865 (m-80) cc_final: 0.7538 (m-10) REVERT: C 863 TYR cc_start: 0.6140 (m-10) cc_final: 0.5579 (m-10) REVERT: C 891 PHE cc_start: 0.8350 (m-10) cc_final: 0.8110 (m-10) REVERT: C 907 MET cc_start: 0.2002 (ppp) cc_final: 0.1144 (tpt) REVERT: C 939 MET cc_start: 0.7826 (tpp) cc_final: 0.7434 (tpt) REVERT: C 1002 LYS cc_start: 0.7399 (ttmp) cc_final: 0.6854 (mtmt) REVERT: C 1009 PHE cc_start: 0.7345 (m-80) cc_final: 0.7142 (t80) REVERT: D 36 PHE cc_start: 0.7037 (t80) cc_final: 0.6529 (t80) REVERT: D 189 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6914 (mm-30) REVERT: D 248 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (m) REVERT: D 361 MET cc_start: 0.8266 (mtp) cc_final: 0.7821 (mtp) REVERT: D 498 LEU cc_start: 0.9032 (pt) cc_final: 0.8477 (pt) REVERT: D 515 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (m-10) REVERT: D 527 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7063 (mmt) REVERT: D 585 MET cc_start: 0.8759 (mmt) cc_final: 0.8420 (mmt) REVERT: E 81 MET cc_start: 0.8976 (ttt) cc_final: 0.8628 (tmm) REVERT: E 88 TRP cc_start: 0.6499 (m100) cc_final: 0.5750 (t60) REVERT: E 116 MET cc_start: 0.0658 (tpp) cc_final: -0.0071 (pmm) REVERT: E 122 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6032 (mm) REVERT: F 88 TRP cc_start: 0.6401 (m100) cc_final: 0.5591 (t60) REVERT: F 115 VAL cc_start: 0.5598 (OUTLIER) cc_final: 0.5301 (m) REVERT: F 116 MET cc_start: 0.0574 (tpp) cc_final: -0.0134 (pmm) outliers start: 71 outliers final: 51 residues processed: 409 average time/residue: 0.1859 time to fit residues: 128.5173 Evaluate side-chains 395 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 408 MET 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 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 196 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 708 MET 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 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 700 TYR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 196 CYS 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 633 ILE 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 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 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: 3.9990 chunk 321 optimal weight: 1.9990 chunk 360 optimal weight: 0.3980 chunk 278 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 106 optimal weight: 0.0370 chunk 6 optimal weight: 7.9990 chunk 356 optimal weight: 0.0020 chunk 257 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108475 restraints weight = 54164.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110241 restraints weight = 35204.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110014 restraints weight = 38220.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111389 restraints weight = 25254.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112322 restraints weight = 21544.944| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31823 Z= 0.113 Angle : 0.855 32.782 42940 Z= 0.372 Chirality : 0.080 2.153 4702 Planarity : 0.003 0.036 5286 Dihedral : 16.674 178.706 5184 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.31 % Favored : 89.50 % Rotamer: Outliers : 2.09 % Allowed : 17.32 % Favored : 80.59 % 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 aren not related in a simple way. whole: -1.79 (0.14), residues: 3762 helix: 0.49 (0.13), residues: 1796 sheet: -3.09 (0.26), residues: 352 loop : -2.75 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 30 TYR 0.030 0.001 TYR D 732 PHE 0.024 0.001 PHE D 517 TRP 0.022 0.001 TRP E 136 HIS 0.013 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00248 (31813) covalent geometry : angle 0.85420 (42920) SS BOND : bond 0.00234 ( 10) SS BOND : angle 1.58837 ( 20) hydrogen bonds : bond 0.03205 ( 1093) hydrogen bonds : angle 4.08783 ( 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 423 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 355 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TRP cc_start: 0.8463 (t-100) cc_final: 0.8146 (t-100) REVERT: A 408 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: A 414 MET cc_start: 0.7716 (ptm) cc_final: 0.7510 (ptp) REVERT: A 638 ASP cc_start: 0.8248 (m-30) cc_final: 0.7464 (t0) REVERT: A 642 GLN cc_start: 0.7448 (mp10) cc_final: 0.6884 (mp10) REVERT: A 678 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 879 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7671 (mmmt) REVERT: A 891 PHE cc_start: 0.8401 (m-10) cc_final: 0.8136 (m-80) REVERT: A 939 MET cc_start: 0.7391 (tpt) cc_final: 0.6928 (ttm) REVERT: A 966 PHE cc_start: 0.7021 (m-80) cc_final: 0.6425 (m-80) REVERT: A 988 MET cc_start: 0.7961 (tmm) cc_final: 0.7619 (tmm) REVERT: A 1009 PHE cc_start: 0.7701 (t80) cc_final: 0.7466 (t80) REVERT: B 41 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.3851 (p90) REVERT: B 189 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6916 (mm-30) REVERT: B 357 THR cc_start: 0.7873 (p) cc_final: 0.7525 (t) REVERT: B 361 MET cc_start: 0.8268 (mtp) cc_final: 0.7713 (mtp) REVERT: B 408 MET cc_start: 0.6869 (mmm) cc_final: 0.6524 (mmp) REVERT: B 515 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: B 573 ILE cc_start: 0.8270 (tp) cc_final: 0.7979 (tp) REVERT: B 585 MET cc_start: 0.8710 (mmt) cc_final: 0.8320 (mmm) REVERT: B 814 PHE cc_start: 0.7237 (t80) cc_final: 0.6756 (t80) REVERT: C 414 MET cc_start: 0.7853 (ptm) cc_final: 0.7560 (ptp) REVERT: C 816 TYR cc_start: 0.7663 (t80) cc_final: 0.7282 (t80) REVERT: C 860 TYR cc_start: 0.7868 (m-80) cc_final: 0.7577 (m-10) REVERT: C 863 TYR cc_start: 0.6197 (m-10) cc_final: 0.5628 (m-10) REVERT: C 864 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 891 PHE cc_start: 0.8322 (m-10) cc_final: 0.8091 (m-10) REVERT: C 939 MET cc_start: 0.7729 (tpp) cc_final: 0.7374 (tpt) REVERT: C 1002 LYS cc_start: 0.7459 (ttmp) cc_final: 0.6925 (mtmt) REVERT: D 36 PHE cc_start: 0.7004 (t80) cc_final: 0.6533 (t80) REVERT: D 189 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7132 (mm-30) REVERT: D 361 MET cc_start: 0.8254 (mtp) cc_final: 0.7832 (mtp) REVERT: D 515 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: D 527 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: D 585 MET cc_start: 0.8738 (mmt) cc_final: 0.8477 (mmt) REVERT: E 81 MET cc_start: 0.8989 (ttt) cc_final: 0.8670 (tmm) REVERT: E 88 TRP cc_start: 0.6357 (m100) cc_final: 0.5652 (t60) REVERT: E 116 MET cc_start: 0.0957 (tpp) cc_final: 0.0066 (pmm) REVERT: E 122 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6102 (mm) REVERT: F 10 TYR cc_start: 0.8136 (m-10) cc_final: 0.7926 (m-10) REVERT: F 72 TYR cc_start: 0.7485 (m-80) cc_final: 0.7204 (m-80) REVERT: F 88 TRP cc_start: 0.6306 (m100) cc_final: 0.5533 (t60) REVERT: F 115 VAL cc_start: 0.5460 (OUTLIER) cc_final: 0.5214 (m) REVERT: F 116 MET cc_start: 0.0558 (tpp) cc_final: -0.0121 (pmm) REVERT: F 130 TYR cc_start: 0.4412 (m-80) cc_final: 0.4187 (m-80) outliers start: 68 outliers final: 47 residues processed: 399 average time/residue: 0.1826 time to fit residues: 124.2896 Evaluate side-chains 379 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 324 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 508 GLN 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 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 196 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 708 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 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 350 ASN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 700 TYR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET 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 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 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 338 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 337 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 985 ASN ** D 359 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105912 restraints weight = 54215.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105242 restraints weight = 37966.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.106187 restraints weight = 36907.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106407 restraints weight = 28261.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107707 restraints weight = 25010.277| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4581 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= 0.148 Angle : 0.868 32.978 42940 Z= 0.380 Chirality : 0.081 2.162 4702 Planarity : 0.003 0.038 5286 Dihedral : 16.565 178.736 5183 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.06 % Favored : 88.76 % Rotamer: Outliers : 1.84 % Allowed : 18.06 % Favored : 80.10 % 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 aren not related in a simple way. whole: -1.71 (0.14), residues: 3762 helix: 0.58 (0.13), residues: 1798 sheet: -3.03 (0.26), residues: 352 loop : -2.75 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.034 0.001 TYR D 732 PHE 0.023 0.001 PHE D 517 TRP 0.021 0.001 TRP E 136 HIS 0.013 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00343 (31813) covalent geometry : angle 0.86715 (42920) SS BOND : bond 0.00439 ( 10) SS BOND : angle 1.64264 ( 20) hydrogen bonds : bond 0.03272 ( 1093) hydrogen bonds : angle 4.08968 ( 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 393 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TRP cc_start: 0.8473 (t-100) cc_final: 0.8143 (t-100) REVERT: A 408 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7091 (mpp) REVERT: A 414 MET cc_start: 0.7761 (ptm) cc_final: 0.7531 (ptp) REVERT: A 638 ASP cc_start: 0.8303 (m-30) cc_final: 0.7605 (t0) REVERT: A 642 GLN cc_start: 0.7479 (mp10) cc_final: 0.7155 (mp10) REVERT: A 678 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8065 (mm-30) REVERT: A 891 PHE cc_start: 0.8357 (m-10) cc_final: 0.8082 (m-80) REVERT: A 939 MET cc_start: 0.7489 (tpt) cc_final: 0.6887 (ttm) REVERT: A 966 PHE cc_start: 0.7021 (m-80) cc_final: 0.6401 (m-80) REVERT: A 988 MET cc_start: 0.7973 (tmm) cc_final: 0.7601 (tmm) REVERT: A 1009 PHE cc_start: 0.7772 (t80) cc_final: 0.7538 (t80) REVERT: B 41 PHE cc_start: 0.5030 (OUTLIER) cc_final: 0.3896 (p90) REVERT: B 357 THR cc_start: 0.7878 (p) cc_final: 0.7543 (t) REVERT: B 361 MET cc_start: 0.8207 (mtp) cc_final: 0.7664 (mtp) REVERT: B 408 MET cc_start: 0.6939 (mmm) cc_final: 0.6653 (mmp) REVERT: B 515 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: B 573 ILE cc_start: 0.8321 (tp) cc_final: 0.8035 (tp) REVERT: B 585 MET cc_start: 0.8758 (mmt) cc_final: 0.8322 (mmm) REVERT: B 814 PHE cc_start: 0.7248 (t80) cc_final: 0.6791 (t80) REVERT: C 414 MET cc_start: 0.7913 (ptm) cc_final: 0.7604 (ptp) REVERT: C 816 TYR cc_start: 0.7678 (t80) cc_final: 0.7294 (t80) REVERT: C 860 TYR cc_start: 0.7891 (m-80) cc_final: 0.7582 (m-10) REVERT: C 863 TYR cc_start: 0.6172 (m-10) cc_final: 0.5584 (m-10) REVERT: C 864 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6706 (tt) REVERT: C 891 PHE cc_start: 0.8312 (m-10) cc_final: 0.8076 (m-10) REVERT: C 907 MET cc_start: 0.0940 (OUTLIER) cc_final: 0.0493 (tpt) REVERT: C 939 MET cc_start: 0.7743 (tpp) cc_final: 0.7384 (tpt) REVERT: C 1002 LYS cc_start: 0.7477 (ttmp) cc_final: 0.6933 (mtmt) REVERT: D 36 PHE cc_start: 0.7101 (t80) cc_final: 0.6641 (t80) REVERT: D 189 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6919 (mm-30) REVERT: D 361 MET cc_start: 0.8281 (mtp) cc_final: 0.7857 (mtp) REVERT: D 515 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: D 527 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7095 (mmt) REVERT: D 585 MET cc_start: 0.8773 (mmt) cc_final: 0.8495 (mmt) REVERT: E 81 MET cc_start: 0.9027 (ttt) cc_final: 0.8661 (tmm) REVERT: E 88 TRP cc_start: 0.6465 (m100) cc_final: 0.5714 (t60) REVERT: E 116 MET cc_start: 0.0702 (tpp) cc_final: -0.0001 (pmm) REVERT: E 122 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6290 (mm) REVERT: E 130 TYR cc_start: 0.4474 (m-80) cc_final: 0.4236 (m-80) REVERT: F 10 TYR cc_start: 0.8156 (m-10) cc_final: 0.7895 (m-10) REVERT: F 72 TYR cc_start: 0.7599 (m-80) cc_final: 0.7066 (m-80) REVERT: F 88 TRP cc_start: 0.6392 (m100) cc_final: 0.5551 (t60) REVERT: F 115 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5076 (m) REVERT: F 116 MET cc_start: 0.0536 (tpp) cc_final: -0.0079 (pmm) REVERT: F 130 TYR cc_start: 0.4427 (m-80) cc_final: 0.4202 (m-80) outliers start: 60 outliers final: 47 residues processed: 372 average time/residue: 0.1793 time to fit residues: 114.3595 Evaluate side-chains 381 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 508 GLN 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 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 196 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 708 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 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 350 ASN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 700 TYR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 864 LEU 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 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU 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 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 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 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 227 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 237 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 359 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106672 restraints weight = 54618.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106450 restraints weight = 36753.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107096 restraints weight = 37953.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107396 restraints weight = 26909.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108350 restraints weight = 24009.538| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31823 Z= 0.139 Angle : 0.863 33.012 42940 Z= 0.377 Chirality : 0.081 2.167 4702 Planarity : 0.003 0.037 5286 Dihedral : 16.468 178.930 5183 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.06 % Favored : 88.81 % Rotamer: Outliers : 2.06 % Allowed : 17.87 % Favored : 80.07 % 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 aren not related in a simple way. whole: -1.67 (0.14), residues: 3762 helix: 0.64 (0.13), residues: 1802 sheet: -3.00 (0.26), residues: 352 loop : -2.78 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 888 TYR 0.030 0.001 TYR D 732 PHE 0.023 0.001 PHE D 517 TRP 0.023 0.001 TRP E 136 HIS 0.013 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00322 (31813) covalent geometry : angle 0.86266 (42920) SS BOND : bond 0.00261 ( 10) SS BOND : angle 1.64853 ( 20) hydrogen bonds : bond 0.03247 ( 1093) hydrogen bonds : angle 4.05314 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.22 seconds wall clock time: 99 minutes 13.11 seconds (5953.11 seconds total)