Starting phenix.real_space_refine on Fri Jun 27 16:14:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss2_40741/06_2025/8ss2_40741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss2_40741/06_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_40741/06_2025/8ss2_40741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss2_40741/06_2025/8ss2_40741.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss2_40741/06_2025/8ss2_40741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss2_40741/06_2025/8ss2_40741.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-1': 3, 'PCW:plan-2': 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-1': 1, 'PCW:plan-2': 2, '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-1': 3, 'PCW:plan-2': 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-1': 1, 'PCW:plan-2': 2, '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-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 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-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 17.01, per 1000 atoms: 0.55 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: 7.81 Conformation dependent library (CDL) restraints added in 3.8 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 38 sheets defined 46.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 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: 11.06 Time building geometry restraints manager: 9.21 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 1035 or resid 1101 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 67.080 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.130 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.050 ------------------------------------------------------------------------------- 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 : 7.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.004 TRP C 861 HIS 0.012 0.003 HIS C 219 PHE 0.052 0.004 PHE E 99 TYR 0.027 0.004 TYR A 702 ARG 0.009 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.29930 ( 1093) hydrogen bonds : angle 10.37714 ( 3201) SS BOND : bond 0.02044 ( 10) SS BOND : angle 3.29454 ( 20) covalent geometry : bond 0.02539 (31813) covalent geometry : angle 1.63617 (42920) *********************** 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 : 4.438 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: 0.4682 time to fit residues: 522.7039 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 : 3.249 ------------------------------------------------------------------------------- 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 319 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 0.0980 chunk 296 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 764 ASN C 950 HIS C 985 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS D 224 ASN D 311 ASN D 318 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 461 ASN E 129 ASN F 129 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107901 restraints weight = 54778.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110321 restraints weight = 38800.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110118 restraints weight = 38232.112| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31823 Z= 0.160 Angle : 0.971 31.879 42940 Z= 0.446 Chirality : 0.088 2.405 4702 Planarity : 0.005 0.058 5286 Dihedral : 19.474 179.948 5190 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.35 % Favored : 88.22 % Rotamer: Outliers : 2.58 % Allowed : 11.00 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.12), residues: 3762 helix: -1.92 (0.11), residues: 1774 sheet: -4.05 (0.23), residues: 386 loop : -3.29 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 766 HIS 0.005 0.001 HIS E 27 PHE 0.028 0.002 PHE C 517 TYR 0.031 0.002 TYR C1001 ARG 0.007 0.001 ARG D 692 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 1093) hydrogen bonds : angle 5.30440 ( 3201) SS BOND : bond 0.00884 ( 10) SS BOND : angle 2.59016 ( 20) covalent geometry : bond 0.00345 (31813) covalent geometry : angle 0.96997 (42920) *********************** 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 573 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 489 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8824 (pt) cc_final: 0.8592 (pt) REVERT: A 186 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 302 GLN cc_start: 0.7564 (pm20) cc_final: 0.7344 (mp10) REVERT: A 414 MET cc_start: 0.7810 (ptm) cc_final: 0.7600 (ptp) REVERT: A 638 ASP cc_start: 0.8428 (m-30) cc_final: 0.8079 (m-30) REVERT: A 678 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 879 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7923 (mmmt) REVERT: A 891 PHE cc_start: 0.8481 (m-10) cc_final: 0.8105 (m-10) REVERT: A 901 PHE cc_start: 0.6797 (m-80) cc_final: 0.6409 (m-10) REVERT: A 939 MET cc_start: 0.7720 (ttm) cc_final: 0.7447 (tpt) REVERT: A 966 PHE cc_start: 0.6921 (m-80) cc_final: 0.6552 (m-80) REVERT: A 1005 TRP cc_start: 0.7159 (p-90) cc_final: 0.6897 (p-90) REVERT: B 46 HIS cc_start: 0.7374 (t-90) cc_final: 0.6997 (t-170) REVERT: B 114 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8271 (ttm170) REVERT: B 133 PHE cc_start: 0.8803 (m-10) cc_final: 0.8394 (m-10) REVERT: B 357 THR cc_start: 0.7983 (p) cc_final: 0.7578 (t) REVERT: B 361 MET cc_start: 0.8223 (mtp) cc_final: 0.7880 (mtp) REVERT: B 392 GLN cc_start: 0.7663 (mp10) cc_final: 0.7300 (mp10) REVERT: B 408 MET cc_start: 0.6703 (mmm) cc_final: 0.6436 (mmm) REVERT: B 527 MET cc_start: 0.7662 (tpp) cc_final: 0.7368 (mmt) REVERT: B 573 ILE cc_start: 0.8700 (tp) cc_final: 0.8437 (tp) REVERT: C 50 LEU cc_start: 0.8690 (pt) cc_final: 0.8381 (pt) REVERT: C 302 GLN cc_start: 0.7573 (pm20) cc_final: 0.7269 (mp10) REVERT: C 412 HIS cc_start: 0.7378 (t-170) cc_final: 0.6722 (t70) REVERT: C 414 MET cc_start: 0.7832 (ptm) cc_final: 0.7566 (ptp) REVERT: C 627 GLU cc_start: 0.8219 (pp20) cc_final: 0.7751 (tm-30) REVERT: C 635 SER cc_start: 0.8978 (t) cc_final: 0.8721 (p) REVERT: C 816 TYR cc_start: 0.7794 (t80) cc_final: 0.7454 (t80) REVERT: C 863 TYR cc_start: 0.5941 (m-10) cc_final: 0.5325 (m-10) REVERT: C 891 PHE cc_start: 0.8325 (m-10) cc_final: 0.7985 (m-80) REVERT: C 907 MET cc_start: 0.2058 (ppp) cc_final: 0.1504 (tpt) REVERT: C 966 PHE cc_start: 0.7026 (m-80) cc_final: 0.6390 (m-80) REVERT: D 33 MET cc_start: 0.8756 (ptm) cc_final: 0.8509 (ptt) REVERT: D 269 GLU cc_start: 0.7603 (tp30) cc_final: 0.7047 (tp30) REVERT: D 357 THR cc_start: 0.7731 (p) cc_final: 0.7506 (t) REVERT: D 361 MET cc_start: 0.8161 (mtp) cc_final: 0.7782 (mtp) REVERT: D 373 TYR cc_start: 0.8891 (p90) cc_final: 0.8642 (p90) REVERT: D 392 GLN cc_start: 0.7469 (mp10) cc_final: 0.7052 (mp10) REVERT: D 408 MET cc_start: 0.7140 (mmm) cc_final: 0.5299 (mmm) REVERT: D 773 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7494 (m) REVERT: E 88 TRP cc_start: 0.6528 (m100) cc_final: 0.5475 (t60) REVERT: E 115 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6482 (m) REVERT: E 116 MET cc_start: 0.1203 (tpp) cc_final: -0.0211 (pmm) REVERT: E 117 TYR cc_start: 0.1452 (m-80) cc_final: -0.1048 (m-80) REVERT: F 84 CYS cc_start: 0.8020 (m) cc_final: 0.7803 (m) REVERT: F 88 TRP cc_start: 0.6491 (m100) cc_final: 0.5485 (t60) REVERT: F 116 MET cc_start: 0.0743 (tpp) cc_final: 0.0214 (pmm) outliers start: 84 outliers final: 28 residues processed: 546 average time/residue: 0.3803 time to fit residues: 344.1171 Evaluate side-chains 414 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 383 time to evaluate : 3.104 ------------------------------------------------------------------------------- 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 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 400 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 167 ASN 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 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 57 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 373 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 726 ASN B 24 GLN B 412 HIS C 112 GLN C 167 ASN C 726 ASN C 985 ASN D 24 GLN D 112 GLN D 246 GLN D 412 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105006 restraints weight = 54975.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106816 restraints weight = 40603.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106720 restraints weight = 40511.850| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 31823 Z= 0.197 Angle : 0.931 32.917 42940 Z= 0.424 Chirality : 0.084 2.272 4702 Planarity : 0.004 0.055 5286 Dihedral : 18.696 177.400 5187 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.70 % Favored : 87.91 % Rotamer: Outliers : 3.04 % Allowed : 13.08 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.13), residues: 3762 helix: -1.08 (0.12), residues: 1784 sheet: -3.90 (0.24), residues: 356 loop : -3.09 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 887 HIS 0.014 0.001 HIS E 27 PHE 0.026 0.002 PHE B 438 TYR 0.027 0.002 TYR C1001 ARG 0.008 0.000 ARG D 692 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1093) hydrogen bonds : angle 4.78911 ( 3201) SS BOND : bond 0.00371 ( 10) SS BOND : angle 2.31352 ( 20) covalent geometry : bond 0.00456 (31813) covalent geometry : angle 0.92938 (42920) *********************** 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 509 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 410 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7569 (ptm160) REVERT: A 50 LEU cc_start: 0.8848 (pt) cc_final: 0.8597 (pt) REVERT: A 414 MET cc_start: 0.7861 (ptm) cc_final: 0.7659 (ptp) REVERT: A 638 ASP cc_start: 0.8418 (m-30) cc_final: 0.7953 (t0) REVERT: A 879 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7914 (mmmt) REVERT: A 891 PHE cc_start: 0.8478 (m-10) cc_final: 0.8230 (m-80) REVERT: A 901 PHE cc_start: 0.6836 (m-80) cc_final: 0.6391 (m-10) REVERT: A 907 MET cc_start: 0.1876 (OUTLIER) cc_final: 0.1173 (tpt) REVERT: A 924 MET cc_start: 0.7495 (pmm) cc_final: 0.7195 (pmm) REVERT: A 939 MET cc_start: 0.7643 (ttm) cc_final: 0.7226 (tpt) REVERT: A 966 PHE cc_start: 0.6915 (m-80) cc_final: 0.6460 (m-80) REVERT: A 988 MET cc_start: 0.8215 (tmm) cc_final: 0.7546 (tmm) REVERT: A 1005 TRP cc_start: 0.7192 (p-90) cc_final: 0.6873 (p-90) REVERT: B 33 MET cc_start: 0.8663 (ptm) cc_final: 0.8365 (ptt) REVERT: B 189 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 357 THR cc_start: 0.7991 (p) cc_final: 0.7672 (t) REVERT: B 361 MET cc_start: 0.8316 (mtp) cc_final: 0.7983 (mtp) REVERT: B 392 GLN cc_start: 0.7746 (mp10) cc_final: 0.7367 (mp10) REVERT: B 404 PRO cc_start: 0.8030 (Cg_endo) cc_final: 0.7805 (Cg_exo) REVERT: B 438 PHE cc_start: 0.8528 (p90) cc_final: 0.8091 (p90) REVERT: B 527 MET cc_start: 0.7716 (tpp) cc_final: 0.7357 (mmt) REVERT: B 573 ILE cc_start: 0.8679 (tp) cc_final: 0.8423 (tp) REVERT: B 585 MET cc_start: 0.8862 (mmt) cc_final: 0.8035 (mmt) REVERT: C 42 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7700 (ptm160) REVERT: C 50 LEU cc_start: 0.8740 (pt) cc_final: 0.8428 (pt) REVERT: C 284 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7982 (mt) REVERT: C 414 MET cc_start: 0.7940 (ptm) cc_final: 0.7649 (ptp) REVERT: C 545 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7179 (ttm170) REVERT: C 627 GLU cc_start: 0.8143 (pp20) cc_final: 0.7868 (tm-30) REVERT: C 635 SER cc_start: 0.9021 (t) cc_final: 0.8797 (p) REVERT: C 863 TYR cc_start: 0.6017 (m-10) cc_final: 0.5288 (m-10) REVERT: C 891 PHE cc_start: 0.8398 (m-10) cc_final: 0.8108 (m-80) REVERT: C 907 MET cc_start: 0.2146 (ppp) cc_final: 0.1391 (tpt) REVERT: C 924 MET cc_start: 0.7404 (ptp) cc_final: 0.6894 (mtm) REVERT: C 966 PHE cc_start: 0.7105 (m-80) cc_final: 0.6435 (m-80) REVERT: C 985 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.6959 (p0) REVERT: C 1002 LYS cc_start: 0.7305 (ttmp) cc_final: 0.6707 (mtmt) REVERT: D 33 MET cc_start: 0.8590 (ptm) cc_final: 0.8325 (ptt) REVERT: D 133 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (m-10) REVERT: D 189 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 357 THR cc_start: 0.7809 (p) cc_final: 0.7597 (t) REVERT: D 361 MET cc_start: 0.8266 (mtp) cc_final: 0.7947 (mtp) REVERT: D 392 GLN cc_start: 0.7460 (mp10) cc_final: 0.7143 (mp10) REVERT: D 408 MET cc_start: 0.6811 (mmm) cc_final: 0.5820 (mmm) REVERT: D 527 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7014 (mmt) REVERT: E 81 MET cc_start: 0.8790 (ttt) cc_final: 0.8533 (tmm) REVERT: E 88 TRP cc_start: 0.6569 (m100) cc_final: 0.5554 (t60) REVERT: E 115 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6498 (m) REVERT: E 116 MET cc_start: 0.0840 (tpp) cc_final: 0.0247 (pmm) REVERT: E 122 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6672 (mm) REVERT: F 88 TRP cc_start: 0.6542 (m100) cc_final: 0.5618 (t60) REVERT: F 116 MET cc_start: 0.0733 (tpp) cc_final: -0.0082 (pmm) outliers start: 99 outliers final: 52 residues processed: 480 average time/residue: 0.4236 time to fit residues: 340.0173 Evaluate side-chains 413 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 352 time to evaluate : 3.648 ------------------------------------------------------------------------------- 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 144 SER 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 541 PHE 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 712 ILE 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 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 341 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain 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 144 SER Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 284 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 C residue 1015 LEU Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain 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 180 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 351 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 46 HIS C 412 HIS ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106388 restraints weight = 54530.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106432 restraints weight = 35670.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106935 restraints weight = 37232.561| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31823 Z= 0.129 Angle : 0.882 32.765 42940 Z= 0.394 Chirality : 0.082 2.230 4702 Planarity : 0.004 0.054 5286 Dihedral : 18.165 178.697 5185 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.82 % Favored : 88.86 % Rotamer: Outliers : 2.46 % Allowed : 14.28 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.13), residues: 3762 helix: -0.60 (0.12), residues: 1780 sheet: -3.77 (0.23), residues: 380 loop : -2.92 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 262 HIS 0.008 0.001 HIS D 412 PHE 0.019 0.001 PHE D 515 TYR 0.025 0.001 TYR C1001 ARG 0.004 0.000 ARG A 888 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1093) hydrogen bonds : angle 4.46870 ( 3201) SS BOND : bond 0.00242 ( 10) SS BOND : angle 1.65786 ( 20) covalent geometry : bond 0.00287 (31813) covalent geometry : angle 0.88108 (42920) *********************** 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 484 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 404 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8608 (pt) cc_final: 0.8367 (pt) REVERT: A 262 TRP cc_start: 0.8555 (t-100) cc_final: 0.8310 (t-100) REVERT: A 414 MET cc_start: 0.7827 (ptm) cc_final: 0.7588 (ptp) REVERT: A 642 GLN cc_start: 0.7500 (mp10) cc_final: 0.7207 (mp10) REVERT: A 879 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7877 (mmmt) REVERT: A 891 PHE cc_start: 0.8475 (m-10) cc_final: 0.8192 (m-80) REVERT: A 907 MET cc_start: 0.1872 (OUTLIER) cc_final: 0.1040 (tpt) REVERT: A 939 MET cc_start: 0.7677 (ttm) cc_final: 0.7372 (tpt) REVERT: A 966 PHE cc_start: 0.6953 (m-80) cc_final: 0.6560 (m-80) REVERT: A 1005 TRP cc_start: 0.7201 (p-90) cc_final: 0.6883 (p-90) REVERT: B 133 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: B 189 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 357 THR cc_start: 0.8047 (p) cc_final: 0.7726 (t) REVERT: B 361 MET cc_start: 0.8251 (mtp) cc_final: 0.7946 (mtp) REVERT: B 392 GLN cc_start: 0.7708 (mp10) cc_final: 0.7333 (mp10) REVERT: B 408 MET cc_start: 0.6723 (mmm) cc_final: 0.6109 (mmm) REVERT: B 527 MET cc_start: 0.7666 (tpp) cc_final: 0.7280 (mmt) REVERT: B 573 ILE cc_start: 0.8479 (tp) cc_final: 0.8223 (tp) REVERT: B 814 PHE cc_start: 0.7203 (t80) cc_final: 0.6973 (t80) REVERT: C 50 LEU cc_start: 0.8484 (pt) cc_final: 0.8163 (pt) REVERT: C 189 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8058 (tp30) REVERT: C 262 TRP cc_start: 0.8376 (t-100) cc_final: 0.8175 (t-100) REVERT: C 414 MET cc_start: 0.7900 (ptm) cc_final: 0.7616 (ptp) REVERT: C 635 SER cc_start: 0.9011 (t) cc_final: 0.8787 (p) REVERT: C 863 TYR cc_start: 0.5980 (m-10) cc_final: 0.5307 (m-10) REVERT: C 891 PHE cc_start: 0.8392 (m-10) cc_final: 0.8094 (m-80) REVERT: C 907 MET cc_start: 0.1925 (ppp) cc_final: 0.1101 (tpt) REVERT: C 924 MET cc_start: 0.7319 (ptp) cc_final: 0.6817 (mtm) REVERT: C 966 PHE cc_start: 0.6994 (m-80) cc_final: 0.6355 (m-80) REVERT: C 985 ASN cc_start: 0.7652 (p0) cc_final: 0.6724 (p0) REVERT: C 1002 LYS cc_start: 0.7194 (ttmp) cc_final: 0.6630 (mtmt) REVERT: C 1009 PHE cc_start: 0.7427 (m-80) cc_final: 0.6972 (t80) REVERT: D 78 ASP cc_start: 0.7491 (p0) cc_final: 0.7134 (p0) REVERT: D 189 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7191 (mm-30) REVERT: D 357 THR cc_start: 0.7843 (p) cc_final: 0.7611 (t) REVERT: D 361 MET cc_start: 0.8283 (mtp) cc_final: 0.7920 (mtp) REVERT: D 515 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: D 527 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6933 (mmt) REVERT: E 81 MET cc_start: 0.8828 (ttt) cc_final: 0.8549 (tmm) REVERT: E 88 TRP cc_start: 0.6652 (m100) cc_final: 0.5628 (t60) REVERT: E 115 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6164 (m) REVERT: E 116 MET cc_start: 0.1042 (tpp) cc_final: 0.0163 (pmm) REVERT: E 122 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6261 (mm) REVERT: F 10 TYR cc_start: 0.8150 (m-80) cc_final: 0.7392 (m-10) REVERT: F 88 TRP cc_start: 0.6583 (m100) cc_final: 0.5649 (t60) REVERT: F 116 MET cc_start: 0.0393 (tpp) cc_final: -0.0367 (pmm) outliers start: 80 outliers final: 48 residues processed: 458 average time/residue: 0.3880 time to fit residues: 296.1030 Evaluate side-chains 415 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 751 LEU Chi-restraints excluded: chain A residue 907 MET 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 133 PHE Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 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 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 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 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 358 ILE Chi-restraints excluded: chain D residue 463 MET 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 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 28 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 275 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 46 HIS C 167 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 246 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105960 restraints weight = 54369.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105929 restraints weight = 36559.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106561 restraints weight = 37346.537| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31823 Z= 0.136 Angle : 0.871 32.832 42940 Z= 0.386 Chirality : 0.081 2.199 4702 Planarity : 0.004 0.042 5286 Dihedral : 17.741 178.603 5185 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.08 % Favored : 88.65 % Rotamer: Outliers : 2.43 % Allowed : 15.97 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 3762 helix: -0.23 (0.12), residues: 1778 sheet: -3.72 (0.23), residues: 378 loop : -2.78 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 262 HIS 0.011 0.001 HIS B 412 PHE 0.032 0.001 PHE B 517 TYR 0.025 0.001 TYR C1001 ARG 0.006 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1093) hydrogen bonds : angle 4.29519 ( 3201) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.56625 ( 20) covalent geometry : bond 0.00307 (31813) covalent geometry : angle 0.87017 (42920) *********************** 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: 79 poor density : 384 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8566 (pt) cc_final: 0.8306 (pt) REVERT: A 262 TRP cc_start: 0.8509 (t-100) cc_final: 0.8277 (t-100) REVERT: A 408 MET cc_start: 0.7362 (tpp) cc_final: 0.7020 (mmm) REVERT: A 414 MET cc_start: 0.7812 (ptm) cc_final: 0.7572 (ptp) REVERT: A 642 GLN cc_start: 0.7489 (mp10) cc_final: 0.7161 (mp10) REVERT: A 879 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7913 (mmmt) REVERT: A 891 PHE cc_start: 0.8461 (m-10) cc_final: 0.8192 (m-80) REVERT: A 966 PHE cc_start: 0.6956 (m-80) cc_final: 0.6575 (m-80) REVERT: A 1005 TRP cc_start: 0.7180 (p-90) cc_final: 0.6971 (p-90) REVERT: B 189 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 357 THR cc_start: 0.7946 (p) cc_final: 0.7640 (t) REVERT: B 361 MET cc_start: 0.8293 (mtp) cc_final: 0.7750 (mtp) REVERT: B 392 GLN cc_start: 0.7709 (mp10) cc_final: 0.7372 (mp10) REVERT: B 408 MET cc_start: 0.6710 (mmm) cc_final: 0.6302 (mmp) REVERT: B 412 HIS cc_start: 0.6929 (t-170) cc_final: 0.6534 (t-170) REVERT: B 425 CYS cc_start: 0.7201 (m) cc_final: 0.6956 (m) REVERT: B 573 ILE cc_start: 0.8444 (tp) cc_final: 0.8175 (tp) REVERT: B 814 PHE cc_start: 0.7295 (t80) cc_final: 0.7059 (t80) REVERT: C 50 LEU cc_start: 0.8455 (pt) cc_final: 0.8126 (pt) REVERT: C 414 MET cc_start: 0.7883 (ptm) cc_final: 0.7534 (ptp) REVERT: C 678 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 863 TYR cc_start: 0.6052 (m-10) cc_final: 0.5386 (m-10) REVERT: C 891 PHE cc_start: 0.8393 (m-10) cc_final: 0.8114 (m-10) REVERT: C 907 MET cc_start: 0.1958 (ppp) cc_final: 0.1070 (tpt) REVERT: C 966 PHE cc_start: 0.7033 (m-80) cc_final: 0.6415 (m-80) REVERT: C 1002 LYS cc_start: 0.7260 (ttmp) cc_final: 0.6701 (mtmt) REVERT: C 1009 PHE cc_start: 0.7430 (m-80) cc_final: 0.7053 (t80) REVERT: D 189 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 361 MET cc_start: 0.8309 (mtp) cc_final: 0.7934 (mtp) REVERT: D 498 LEU cc_start: 0.9063 (pt) cc_final: 0.8772 (pt) REVERT: D 515 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: D 527 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6908 (mmt) REVERT: E 81 MET cc_start: 0.8912 (ttt) cc_final: 0.8615 (tmm) REVERT: E 88 TRP cc_start: 0.6590 (m100) cc_final: 0.5670 (t60) REVERT: E 115 VAL cc_start: 0.6407 (OUTLIER) cc_final: 0.6114 (m) REVERT: E 116 MET cc_start: 0.1029 (tpp) cc_final: 0.0188 (pmm) REVERT: E 122 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6389 (mm) REVERT: F 88 TRP cc_start: 0.6489 (m100) cc_final: 0.5511 (t60) REVERT: F 115 VAL cc_start: 0.6442 (OUTLIER) cc_final: 0.6115 (m) REVERT: F 116 MET cc_start: 0.0570 (tpp) cc_final: -0.0407 (pmm) outliers start: 79 outliers final: 50 residues processed: 437 average time/residue: 0.3994 time to fit residues: 292.4544 Evaluate side-chains 393 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 3.381 ------------------------------------------------------------------------------- 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 167 ASN Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL 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 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 400 ILE Chi-restraints excluded: chain B residue 538 VAL 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 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 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 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 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 125 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 112 optimal weight: 0.0670 chunk 168 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 46 HIS C 167 ASN C 335 GLN C 985 ASN 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 = 0.3956 r_free = 0.3956 target = 0.142572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105499 restraints weight = 54684.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106363 restraints weight = 36495.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106651 restraints weight = 37285.326| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31823 Z= 0.143 Angle : 0.869 32.916 42940 Z= 0.384 Chirality : 0.081 2.186 4702 Planarity : 0.004 0.036 5286 Dihedral : 17.479 178.733 5185 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.93 % Favored : 88.81 % Rotamer: Outliers : 2.67 % Allowed : 16.31 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3762 helix: 0.02 (0.13), residues: 1776 sheet: -3.48 (0.25), residues: 354 loop : -2.77 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 262 HIS 0.011 0.001 HIS F 107 PHE 0.029 0.001 PHE D 517 TYR 0.025 0.001 TYR C1001 ARG 0.003 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 1093) hydrogen bonds : angle 4.23390 ( 3201) SS BOND : bond 0.00226 ( 10) SS BOND : angle 1.53371 ( 20) covalent geometry : bond 0.00329 (31813) covalent geometry : angle 0.86823 (42920) *********************** 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 442 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8469 (pt) cc_final: 0.8181 (pt) REVERT: A 262 TRP cc_start: 0.8468 (t-100) cc_final: 0.8253 (t-100) REVERT: A 414 MET cc_start: 0.7791 (ptm) cc_final: 0.7570 (ptp) REVERT: A 642 GLN cc_start: 0.7545 (mp10) cc_final: 0.7188 (mp10) REVERT: A 879 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7882 (mmmt) REVERT: A 891 PHE cc_start: 0.8440 (m-10) cc_final: 0.8187 (m-80) REVERT: A 939 MET cc_start: 0.7554 (tpt) cc_final: 0.7074 (ttt) REVERT: A 966 PHE cc_start: 0.7056 (m-80) cc_final: 0.6377 (m-80) REVERT: A 1009 PHE cc_start: 0.7806 (m-80) cc_final: 0.7547 (t80) REVERT: B 189 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 357 THR cc_start: 0.7959 (p) cc_final: 0.7606 (t) REVERT: B 361 MET cc_start: 0.8312 (mtp) cc_final: 0.7757 (mtp) REVERT: B 392 GLN cc_start: 0.7630 (mp10) cc_final: 0.7351 (mp10) REVERT: B 408 MET cc_start: 0.6595 (mmm) cc_final: 0.6157 (mmp) REVERT: B 412 HIS cc_start: 0.6970 (t-170) cc_final: 0.6742 (t-170) REVERT: B 425 CYS cc_start: 0.7133 (m) cc_final: 0.6918 (m) REVERT: B 573 ILE cc_start: 0.8403 (tp) cc_final: 0.8140 (tp) REVERT: B 585 MET cc_start: 0.8862 (mmt) cc_final: 0.8086 (mmt) REVERT: B 814 PHE cc_start: 0.7342 (t80) cc_final: 0.7099 (t80) REVERT: C 414 MET cc_start: 0.7896 (ptm) cc_final: 0.7552 (ptp) REVERT: C 863 TYR cc_start: 0.6049 (m-10) cc_final: 0.5414 (m-10) REVERT: C 891 PHE cc_start: 0.8359 (m-10) cc_final: 0.8016 (m-10) REVERT: C 907 MET cc_start: 0.2104 (ppp) cc_final: 0.1115 (tpt) REVERT: C 924 MET cc_start: 0.7675 (ptp) cc_final: 0.7189 (mtm) REVERT: C 966 PHE cc_start: 0.7064 (m-80) cc_final: 0.6493 (m-80) REVERT: C 1002 LYS cc_start: 0.7358 (ttmp) cc_final: 0.6782 (mtmt) REVERT: C 1009 PHE cc_start: 0.7403 (m-80) cc_final: 0.7102 (t80) REVERT: D 361 MET cc_start: 0.8340 (mtp) cc_final: 0.7944 (mtp) REVERT: D 498 LEU cc_start: 0.9058 (pt) cc_final: 0.8560 (pt) REVERT: D 515 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: D 527 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7120 (mmt) REVERT: E 81 MET cc_start: 0.8946 (ttt) cc_final: 0.8612 (tmm) REVERT: E 88 TRP cc_start: 0.6571 (m100) cc_final: 0.5691 (t60) REVERT: E 115 VAL cc_start: 0.6267 (OUTLIER) cc_final: 0.6007 (m) REVERT: E 116 MET cc_start: 0.0989 (tpp) cc_final: 0.0287 (pmm) REVERT: E 122 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6171 (mm) REVERT: F 88 TRP cc_start: 0.6478 (m100) cc_final: 0.5508 (t60) REVERT: F 115 VAL cc_start: 0.6269 (OUTLIER) cc_final: 0.5972 (m) REVERT: F 116 MET cc_start: 0.0835 (tpp) cc_final: -0.0167 (pmm) outliers start: 87 outliers final: 59 residues processed: 416 average time/residue: 0.4026 time to fit residues: 280.7990 Evaluate side-chains 392 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 3.470 ------------------------------------------------------------------------------- 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 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU 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 922 LEU Chi-restraints excluded: chain A residue 960 PHE 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 358 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 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 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 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 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 121 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 253 optimal weight: 0.0770 chunk 352 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 281 optimal weight: 0.0870 chunk 128 optimal weight: 0.4980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 46 HIS C 167 ASN C 985 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.107651 restraints weight = 54187.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107593 restraints weight = 36271.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108016 restraints weight = 39148.463| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31823 Z= 0.115 Angle : 0.857 32.787 42940 Z= 0.376 Chirality : 0.080 2.167 4702 Planarity : 0.003 0.037 5286 Dihedral : 17.171 178.775 5185 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.55 % Favored : 89.23 % Rotamer: Outliers : 2.33 % Allowed : 16.92 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.14), residues: 3762 helix: 0.20 (0.13), residues: 1794 sheet: -3.41 (0.23), residues: 410 loop : -2.68 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 262 HIS 0.013 0.001 HIS F 107 PHE 0.027 0.001 PHE D 517 TYR 0.025 0.001 TYR C1001 ARG 0.007 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 1093) hydrogen bonds : angle 4.13867 ( 3201) SS BOND : bond 0.00177 ( 10) SS BOND : angle 1.57005 ( 20) covalent geometry : bond 0.00259 (31813) covalent geometry : angle 0.85631 (42920) *********************** 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 447 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8267 (pt) cc_final: 0.7980 (pt) REVERT: A 414 MET cc_start: 0.7892 (ptm) cc_final: 0.7600 (ptp) REVERT: A 642 GLN cc_start: 0.7530 (mp10) cc_final: 0.7076 (mp10) REVERT: A 866 GLU cc_start: 0.7134 (tp30) cc_final: 0.6891 (tm-30) REVERT: A 879 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7601 (mmmt) REVERT: A 891 PHE cc_start: 0.8431 (m-10) cc_final: 0.8130 (m-80) REVERT: A 939 MET cc_start: 0.7563 (tpt) cc_final: 0.7000 (ttm) REVERT: A 966 PHE cc_start: 0.7065 (m-80) cc_final: 0.6374 (m-80) REVERT: B 41 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.3757 (p90) REVERT: B 189 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6957 (mm-30) REVERT: B 357 THR cc_start: 0.7967 (p) cc_final: 0.7624 (t) REVERT: B 361 MET cc_start: 0.8260 (mtp) cc_final: 0.7700 (mtp) REVERT: B 408 MET cc_start: 0.6576 (mmm) cc_final: 0.6271 (mmp) REVERT: B 573 ILE cc_start: 0.8300 (tp) cc_final: 0.8069 (tp) REVERT: B 585 MET cc_start: 0.8795 (mmt) cc_final: 0.8047 (mmt) REVERT: B 814 PHE cc_start: 0.7380 (t80) cc_final: 0.6938 (t80) REVERT: C 414 MET cc_start: 0.7892 (ptm) cc_final: 0.7541 (ptp) REVERT: C 638 ASP cc_start: 0.8414 (m-30) cc_final: 0.7585 (t0) REVERT: C 639 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7891 (tt) REVERT: C 647 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: C 863 TYR cc_start: 0.6027 (m-10) cc_final: 0.5499 (m-10) REVERT: C 891 PHE cc_start: 0.8324 (m-10) cc_final: 0.8093 (m-10) REVERT: C 907 MET cc_start: 0.1944 (ppp) cc_final: 0.1089 (tpt) REVERT: C 924 MET cc_start: 0.7647 (ptp) cc_final: 0.7090 (mtm) REVERT: C 939 MET cc_start: 0.7448 (tpt) cc_final: 0.6931 (ttm) REVERT: C 966 PHE cc_start: 0.7090 (m-80) cc_final: 0.6449 (m-80) REVERT: C 1002 LYS cc_start: 0.7283 (ttmp) cc_final: 0.6739 (mtmt) REVERT: C 1009 PHE cc_start: 0.7356 (m-80) cc_final: 0.7085 (t80) REVERT: D 78 ASP cc_start: 0.7509 (p0) cc_final: 0.7251 (p0) REVERT: D 189 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6974 (mm-30) REVERT: D 361 MET cc_start: 0.8291 (mtp) cc_final: 0.7886 (mtp) REVERT: D 498 LEU cc_start: 0.9039 (pt) cc_final: 0.8688 (pt) REVERT: D 515 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: D 527 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7023 (mmt) REVERT: E 81 MET cc_start: 0.8924 (ttt) cc_final: 0.8577 (tmm) REVERT: E 88 TRP cc_start: 0.6551 (m100) cc_final: 0.5674 (t60) REVERT: E 115 VAL cc_start: 0.5844 (OUTLIER) cc_final: 0.5591 (m) REVERT: E 116 MET cc_start: 0.0673 (tpp) cc_final: 0.0048 (pmm) REVERT: E 122 ILE cc_start: 0.6571 (mp) cc_final: 0.6150 (mm) REVERT: F 88 TRP cc_start: 0.6435 (m100) cc_final: 0.5536 (t60) REVERT: F 115 VAL cc_start: 0.6082 (OUTLIER) cc_final: 0.5798 (m) REVERT: F 116 MET cc_start: 0.0614 (tpp) cc_final: -0.0140 (pmm) outliers start: 76 outliers final: 50 residues processed: 426 average time/residue: 0.3804 time to fit residues: 272.5338 Evaluate side-chains 387 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 3.397 ------------------------------------------------------------------------------- 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 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 543 VAL 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 960 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 706 SER 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 167 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 960 PHE 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 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 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 155 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 344 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 412 HIS A 954 HIS B 46 HIS B 337 GLN C 167 ASN C 182 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 101 HIS F 107 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.144469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108496 restraints weight = 54451.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107238 restraints weight = 36449.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108319 restraints weight = 36809.832| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31823 Z= 0.118 Angle : 0.858 32.756 42940 Z= 0.374 Chirality : 0.080 2.154 4702 Planarity : 0.003 0.034 5286 Dihedral : 16.901 178.745 5185 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.58 % Favored : 89.21 % Rotamer: Outliers : 2.15 % Allowed : 17.51 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3762 helix: 0.38 (0.13), residues: 1794 sheet: -3.16 (0.25), residues: 384 loop : -2.66 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 262 HIS 0.012 0.001 HIS E 107 PHE 0.033 0.001 PHE A 937 TYR 0.024 0.001 TYR B 702 ARG 0.005 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 1093) hydrogen bonds : angle 4.10865 ( 3201) SS BOND : bond 0.00801 ( 10) SS BOND : angle 1.59970 ( 20) covalent geometry : bond 0.00267 (31813) covalent geometry : angle 0.85754 (42920) *********************** 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 423 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8215 (pt) cc_final: 0.7913 (pt) REVERT: A 414 MET cc_start: 0.7854 (ptm) cc_final: 0.7593 (ptp) REVERT: A 642 GLN cc_start: 0.7471 (mp10) cc_final: 0.7018 (mp10) REVERT: A 816 TYR cc_start: 0.7485 (t80) cc_final: 0.7104 (t80) REVERT: A 866 GLU cc_start: 0.7088 (tp30) cc_final: 0.6842 (tm-30) REVERT: A 879 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7581 (mmmt) REVERT: A 891 PHE cc_start: 0.8378 (m-10) cc_final: 0.8109 (m-80) REVERT: A 939 MET cc_start: 0.7507 (tpt) cc_final: 0.6974 (ttm) REVERT: A 966 PHE cc_start: 0.7017 (m-80) cc_final: 0.6382 (m-80) REVERT: A 1002 LYS cc_start: 0.7917 (ttmp) cc_final: 0.7277 (mtmt) REVERT: B 41 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.3671 (p90) REVERT: B 303 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6938 (mmp80) REVERT: B 357 THR cc_start: 0.7901 (p) cc_final: 0.7555 (t) REVERT: B 361 MET cc_start: 0.8248 (mtp) cc_final: 0.7716 (mtp) REVERT: B 573 ILE cc_start: 0.8332 (tp) cc_final: 0.8061 (tp) REVERT: B 585 MET cc_start: 0.8770 (mmt) cc_final: 0.8156 (mmt) REVERT: B 814 PHE cc_start: 0.7399 (t80) cc_final: 0.6948 (t80) REVERT: C 414 MET cc_start: 0.7855 (ptm) cc_final: 0.7542 (ptp) REVERT: C 638 ASP cc_start: 0.8329 (m-30) cc_final: 0.7612 (t0) REVERT: C 863 TYR cc_start: 0.6011 (m-10) cc_final: 0.5459 (m-10) REVERT: C 891 PHE cc_start: 0.8320 (m-10) cc_final: 0.8095 (m-10) REVERT: C 907 MET cc_start: 0.2114 (ppp) cc_final: 0.1223 (tpt) REVERT: C 924 MET cc_start: 0.7601 (ptp) cc_final: 0.7050 (mtm) REVERT: C 939 MET cc_start: 0.7460 (tpt) cc_final: 0.6935 (ttm) REVERT: C 966 PHE cc_start: 0.7076 (m-80) cc_final: 0.6478 (m-80) REVERT: C 1002 LYS cc_start: 0.7312 (ttmp) cc_final: 0.6795 (mtmt) REVERT: C 1009 PHE cc_start: 0.7388 (m-80) cc_final: 0.7150 (t80) REVERT: D 78 ASP cc_start: 0.7497 (p0) cc_final: 0.7270 (p0) REVERT: D 189 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6911 (mm-30) REVERT: D 361 MET cc_start: 0.8249 (mtp) cc_final: 0.7852 (mtp) REVERT: D 515 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: D 527 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7010 (mmt) REVERT: E 81 MET cc_start: 0.8919 (ttt) cc_final: 0.8581 (tmm) REVERT: E 88 TRP cc_start: 0.6497 (m100) cc_final: 0.5686 (t60) REVERT: E 115 VAL cc_start: 0.5696 (OUTLIER) cc_final: 0.5434 (m) REVERT: E 116 MET cc_start: 0.0639 (tpp) cc_final: -0.0055 (pmm) REVERT: E 122 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6061 (mm) REVERT: F 10 TYR cc_start: 0.8140 (m-10) cc_final: 0.7904 (m-10) REVERT: F 88 TRP cc_start: 0.6409 (m100) cc_final: 0.5483 (t60) REVERT: F 105 TYR cc_start: 0.6085 (t80) cc_final: 0.5484 (m-10) REVERT: F 115 VAL cc_start: 0.5794 (OUTLIER) cc_final: 0.5495 (m) REVERT: F 116 MET cc_start: 0.0680 (tpp) cc_final: -0.0203 (pmm) outliers start: 70 outliers final: 49 residues processed: 402 average time/residue: 0.3785 time to fit residues: 258.2086 Evaluate side-chains 388 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 3.195 ------------------------------------------------------------------------------- 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 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 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 683 VAL 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 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 274 HIS 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 639 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 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 75 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS 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 123 MET Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 330 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 320 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 287 optimal weight: 0.0770 chunk 348 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 168 optimal weight: 0.3980 chunk 247 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 412 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.145093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108735 restraints weight = 54250.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108360 restraints weight = 37859.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110932 restraints weight = 30369.321| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31823 Z= 0.116 Angle : 0.854 32.722 42940 Z= 0.372 Chirality : 0.080 2.145 4702 Planarity : 0.003 0.040 5286 Dihedral : 16.613 178.794 5184 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.42 % Favored : 89.39 % Rotamer: Outliers : 2.06 % Allowed : 17.97 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3762 helix: 0.56 (0.13), residues: 1796 sheet: -3.09 (0.25), residues: 388 loop : -2.66 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 262 HIS 0.013 0.001 HIS E 107 PHE 0.036 0.001 PHE A 937 TYR 0.025 0.001 TYR C 816 ARG 0.010 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 1093) hydrogen bonds : angle 4.05148 ( 3201) SS BOND : bond 0.00188 ( 10) SS BOND : angle 1.63946 ( 20) covalent geometry : bond 0.00260 (31813) covalent geometry : angle 0.85377 (42920) *********************** 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 433 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 366 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7940 (ptm) cc_final: 0.7679 (ptp) REVERT: A 638 ASP cc_start: 0.8304 (m-30) cc_final: 0.7589 (t0) REVERT: A 642 GLN cc_start: 0.7431 (mp10) cc_final: 0.7087 (mp10) REVERT: A 816 TYR cc_start: 0.7526 (t80) cc_final: 0.7268 (t80) REVERT: A 866 GLU cc_start: 0.7158 (tp30) cc_final: 0.6916 (tm-30) REVERT: A 879 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7642 (mmmt) REVERT: A 891 PHE cc_start: 0.8398 (m-10) cc_final: 0.8145 (m-80) REVERT: A 939 MET cc_start: 0.7511 (tpt) cc_final: 0.6961 (ttm) REVERT: A 966 PHE cc_start: 0.7027 (m-80) cc_final: 0.6394 (m-80) REVERT: A 1001 TYR cc_start: 0.8481 (p90) cc_final: 0.8239 (p90) REVERT: B 41 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3784 (p90) REVERT: B 189 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 357 THR cc_start: 0.7916 (p) cc_final: 0.7572 (t) REVERT: B 361 MET cc_start: 0.8214 (mtp) cc_final: 0.7657 (mtp) REVERT: B 573 ILE cc_start: 0.8293 (tp) cc_final: 0.8027 (tp) REVERT: B 585 MET cc_start: 0.8806 (mmt) cc_final: 0.8155 (mmt) REVERT: B 814 PHE cc_start: 0.7403 (t80) cc_final: 0.6961 (t80) REVERT: C 414 MET cc_start: 0.7868 (ptm) cc_final: 0.7553 (ptp) REVERT: C 638 ASP cc_start: 0.8344 (m-30) cc_final: 0.7662 (t70) REVERT: C 863 TYR cc_start: 0.6015 (m-10) cc_final: 0.5681 (m-10) REVERT: C 864 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6636 (tt) REVERT: C 891 PHE cc_start: 0.8271 (m-10) cc_final: 0.8051 (m-10) REVERT: C 966 PHE cc_start: 0.7073 (m-80) cc_final: 0.6588 (m-80) REVERT: C 986 ASP cc_start: 0.8140 (p0) cc_final: 0.7844 (t70) REVERT: C 1002 LYS cc_start: 0.7347 (ttmp) cc_final: 0.6883 (mtmt) REVERT: C 1009 PHE cc_start: 0.7292 (m-80) cc_final: 0.7080 (t80) REVERT: D 78 ASP cc_start: 0.7479 (p0) cc_final: 0.7258 (p0) REVERT: D 189 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6831 (mm-30) REVERT: D 361 MET cc_start: 0.8257 (mtp) cc_final: 0.7868 (mtp) REVERT: D 515 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7946 (m-10) REVERT: D 527 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7038 (mmt) REVERT: E 81 MET cc_start: 0.8926 (ttt) cc_final: 0.8580 (tmm) REVERT: E 88 TRP cc_start: 0.6410 (m100) cc_final: 0.5614 (t60) REVERT: E 115 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5123 (m) REVERT: E 116 MET cc_start: 0.0789 (tpp) cc_final: 0.0164 (pmm) REVERT: E 122 ILE cc_start: 0.6497 (mp) cc_final: 0.6114 (mm) REVERT: F 10 TYR cc_start: 0.8137 (m-10) cc_final: 0.7921 (m-10) REVERT: F 72 TYR cc_start: 0.7216 (m-80) cc_final: 0.6517 (m-80) REVERT: F 88 TRP cc_start: 0.6390 (m100) cc_final: 0.5490 (t60) REVERT: F 105 TYR cc_start: 0.5897 (t80) cc_final: 0.5340 (m-10) REVERT: F 115 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5292 (m) REVERT: F 116 MET cc_start: 0.0494 (tpp) cc_final: -0.0244 (pmm) REVERT: F 130 TYR cc_start: 0.4419 (m-80) cc_final: 0.4189 (m-80) outliers start: 67 outliers final: 51 residues processed: 413 average time/residue: 0.3823 time to fit residues: 268.4178 Evaluate side-chains 391 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 3.152 ------------------------------------------------------------------------------- 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 299 LEU 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 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 706 SER 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 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 274 HIS 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 639 LEU Chi-restraints excluded: chain C residue 645 ILE 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 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 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 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS 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 125 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 191 optimal weight: 0.0170 chunk 112 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- 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** B 337 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107812 restraints weight = 54229.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107953 restraints weight = 36619.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109548 restraints weight = 29654.137| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4628 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= 0.138 Angle : 0.870 32.841 42940 Z= 0.379 Chirality : 0.081 2.152 4702 Planarity : 0.003 0.039 5286 Dihedral : 16.500 178.812 5184 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.61 % Favored : 89.15 % Rotamer: Outliers : 2.06 % Allowed : 18.49 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3762 helix: 0.66 (0.13), residues: 1794 sheet: -2.97 (0.26), residues: 374 loop : -2.71 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 136 HIS 0.013 0.001 HIS E 107 PHE 0.034 0.001 PHE A 937 TYR 0.026 0.001 TYR B 702 ARG 0.004 0.000 ARG A 888 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1093) hydrogen bonds : angle 4.06231 ( 3201) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.65742 ( 20) covalent geometry : bond 0.00321 (31813) covalent geometry : angle 0.86949 (42920) ********************** 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 418 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 351 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7913 (ptm) cc_final: 0.7647 (ptp) REVERT: A 638 ASP cc_start: 0.8316 (m-30) cc_final: 0.7579 (t0) REVERT: A 642 GLN cc_start: 0.7428 (mp10) cc_final: 0.7080 (mp10) REVERT: A 816 TYR cc_start: 0.7503 (t80) cc_final: 0.7264 (t80) REVERT: A 879 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7690 (mmmt) REVERT: A 891 PHE cc_start: 0.8399 (m-10) cc_final: 0.8134 (m-80) REVERT: A 939 MET cc_start: 0.7466 (tpt) cc_final: 0.6946 (ttm) REVERT: A 966 PHE cc_start: 0.6970 (m-80) cc_final: 0.6391 (m-80) REVERT: B 41 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.3885 (p90) REVERT: B 189 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 337 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: B 357 THR cc_start: 0.7912 (p) cc_final: 0.7569 (t) REVERT: B 361 MET cc_start: 0.8241 (mtp) cc_final: 0.7686 (mtp) REVERT: B 573 ILE cc_start: 0.8299 (tp) cc_final: 0.8024 (tp) REVERT: B 585 MET cc_start: 0.8839 (mmt) cc_final: 0.8170 (mmt) REVERT: B 814 PHE cc_start: 0.7426 (t80) cc_final: 0.6978 (t80) REVERT: C 414 MET cc_start: 0.7891 (ptm) cc_final: 0.7577 (ptp) REVERT: C 638 ASP cc_start: 0.8352 (m-30) cc_final: 0.7697 (t70) REVERT: C 863 TYR cc_start: 0.6123 (m-10) cc_final: 0.5779 (m-10) REVERT: C 864 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6718 (tt) REVERT: C 891 PHE cc_start: 0.8312 (m-10) cc_final: 0.8088 (m-10) REVERT: C 907 MET cc_start: 0.1128 (OUTLIER) cc_final: 0.0512 (tpt) REVERT: C 966 PHE cc_start: 0.7041 (m-80) cc_final: 0.6682 (m-80) REVERT: C 1002 LYS cc_start: 0.7432 (ttmp) cc_final: 0.6951 (mtmt) REVERT: D 361 MET cc_start: 0.8230 (mtp) cc_final: 0.7841 (mtp) REVERT: D 515 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: D 527 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7096 (mmt) REVERT: E 81 MET cc_start: 0.8964 (ttt) cc_final: 0.8609 (tmm) REVERT: E 88 TRP cc_start: 0.6429 (m100) cc_final: 0.5711 (t60) REVERT: E 115 VAL cc_start: 0.5118 (OUTLIER) cc_final: 0.4878 (m) REVERT: E 116 MET cc_start: 0.0728 (tpp) cc_final: 0.0071 (pmm) REVERT: E 122 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6049 (mm) REVERT: F 10 TYR cc_start: 0.8136 (m-10) cc_final: 0.7892 (m-10) REVERT: F 72 TYR cc_start: 0.7179 (m-80) cc_final: 0.6612 (m-80) REVERT: F 88 TRP cc_start: 0.6362 (m100) cc_final: 0.5521 (t60) REVERT: F 115 VAL cc_start: 0.5517 (OUTLIER) cc_final: 0.5173 (m) REVERT: F 116 MET cc_start: 0.0279 (tpp) cc_final: -0.0378 (pmm) REVERT: F 130 TYR cc_start: 0.4407 (m-80) cc_final: 0.4186 (m-80) outliers start: 67 outliers final: 51 residues processed: 398 average time/residue: 0.3890 time to fit residues: 264.4895 Evaluate side-chains 392 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 332 time to evaluate : 3.377 ------------------------------------------------------------------------------- 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 299 LEU 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 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 645 ILE 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 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 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS 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 334 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 330 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 286 optimal weight: 0.0770 chunk 329 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN E 107 HIS F 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108545 restraints weight = 54143.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108057 restraints weight = 35322.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108953 restraints weight = 35135.333| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31823 Z= 0.123 Angle : 0.866 32.788 42940 Z= 0.376 Chirality : 0.081 2.151 4702 Planarity : 0.003 0.039 5286 Dihedral : 16.452 178.862 5184 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.55 % Favored : 89.23 % Rotamer: Outliers : 2.00 % Allowed : 18.73 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3762 helix: 0.73 (0.13), residues: 1796 sheet: -2.93 (0.25), residues: 372 loop : -2.72 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 136 HIS 0.013 0.001 HIS E 107 PHE 0.033 0.001 PHE A 937 TYR 0.024 0.001 TYR B 702 ARG 0.005 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 1093) hydrogen bonds : angle 4.03700 ( 3201) SS BOND : bond 0.00238 ( 10) SS BOND : angle 1.63475 ( 20) covalent geometry : bond 0.00282 (31813) covalent geometry : angle 0.86551 (42920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10677.15 seconds wall clock time: 188 minutes 42.64 seconds (11322.64 seconds total)