Starting phenix.real_space_refine on Sat Aug 10 11:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/08_2024/8ss8_40747.cif" } resolution = 2.81 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= 0.009 sd= 0.188 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 S 140 5.16 5 Na 2 4.78 5 C 18450 2.51 5 N 4608 2.21 5 O 5261 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Time to flip residues: 1.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28487 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 946} 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: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 946} 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: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 203 Unusual residues: {' NA': 2, '6ZP': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 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': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 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: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 201 Unusual residues: {'6ZP': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 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': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 16.87, per 1000 atoms: 0.59 Number of scatterers: 28487 At special positions: 0 Unit cell: (117.475, 158.175, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 140 16.00 P 14 15.00 Na 2 11.00 F 12 9.00 O 5261 8.00 N 4608 7.00 C 18450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.32 Conformation dependent library (CDL) restraints added in 5.0 seconds 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 36 sheets defined 48.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.541A pdb=" N SER A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.580A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.820A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.666A pdb=" N ILE A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.003A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.624A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.693A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.938A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.766A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.785A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 629 removed outlier: 3.868A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 609 " --> pdb=" O TRP A 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.689A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.637A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.537A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 793 through 819 removed outlier: 3.650A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.579A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 928 removed outlier: 3.891A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 950 removed outlier: 3.670A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 4.109A pdb=" N VAL A 961 " --> pdb=" O ILE A 957 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1032 removed outlier: 3.627A pdb=" N ALA A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.588A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.554A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.506A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.837A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.623A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.562A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.726A pdb=" N GLY B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.093A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.809A pdb=" N SER B 516 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 517' Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.546A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 626 removed outlier: 3.558A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.651A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.690A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 793 through 814 removed outlier: 3.515A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.540A pdb=" N SER C 37 " --> pdb=" O MET C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.578A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.820A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.666A pdb=" N ILE C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.003A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.624A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.692A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.939A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.785A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 629 removed outlier: 3.868A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 609 " --> pdb=" O TRP C 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.689A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.636A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.538A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 793 through 819 removed outlier: 3.650A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 819 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.578A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 847 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 858 " --> pdb=" O ILE C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 928 removed outlier: 3.891A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 950 removed outlier: 3.669A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 4.111A pdb=" N VAL C 961 " --> pdb=" O ILE C 957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN C 990 " --> pdb=" O ASP C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1032 removed outlier: 3.627A pdb=" N ALA C1010 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 removed outlier: 3.587A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.553A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.506A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 removed outlier: 3.836A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.622A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.563A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 385 through 389 removed outlier: 3.726A pdb=" N GLY D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.093A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.808A pdb=" N SER D 516 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 517' Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.546A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 626 removed outlier: 3.558A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.651A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.691A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 793 through 814 removed outlier: 3.516A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.088A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 220 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE A 245 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE A 222 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 220 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE A 245 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE A 222 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.509A pdb=" N GLY A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.522A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.522A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.598A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 862 through 868 Processing sheet with id=AB1, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 50 removed outlier: 7.024A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.227A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.521A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.595A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.685A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.458A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.088A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.501A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.522A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.522A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.598A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 862 through 868 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AD2, first strand: chain 'D' and resid 45 through 50 removed outlier: 7.024A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.227A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.521A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.596A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD7, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AD8, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.685A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.458A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1336 hydrogen bonds defined for protein. 3921 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: 10.94 Time building geometry restraints manager: 11.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8 1.16 - 1.33: 7169 1.33 - 1.50: 11897 1.50 - 1.67: 9757 1.67 - 1.85: 249 Bond restraints: 29080 Sorted by residual: bond pdb=" C14 CLR D1103 " pdb=" C8 CLR D1103 " ideal model delta sigma weight residual 1.519 0.984 0.535 2.00e-02 2.50e+03 7.14e+02 bond pdb=" C14 CLR B1103 " pdb=" C8 CLR B1103 " ideal model delta sigma weight residual 1.519 0.985 0.534 2.00e-02 2.50e+03 7.12e+02 bond pdb=" C11 CLR D1103 " pdb=" C12 CLR D1103 " ideal model delta sigma weight residual 1.531 1.098 0.433 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C11 CLR B1103 " pdb=" C12 CLR B1103 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C7 CLR B1103 " pdb=" C8 CLR B1103 " ideal model delta sigma weight residual 1.525 1.209 0.316 2.00e-02 2.50e+03 2.49e+02 ... (remaining 29075 not shown) Histogram of bond angle deviations from ideal: 86.71 - 104.54: 363 104.54 - 122.37: 34915 122.37 - 140.20: 3962 140.20 - 158.03: 0 158.03 - 175.86: 4 Bond angle restraints: 39244 Sorted by residual: angle pdb=" C14 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C18 CLR D1103 " ideal model delta sigma weight residual 112.24 87.70 24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" C12 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C18 CLR B1103 " ideal model delta sigma weight residual 111.01 86.71 24.30 3.00e+00 1.11e-01 6.56e+01 angle pdb=" C12 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C18 CLR D1103 " ideal model delta sigma weight residual 111.01 87.49 23.52 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C14 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C18 CLR B1103 " ideal model delta sigma weight residual 112.24 88.76 23.48 3.00e+00 1.11e-01 6.13e+01 angle pdb=" N VAL B 165 " pdb=" CA VAL B 165 " pdb=" C VAL B 165 " ideal model delta sigma weight residual 112.43 106.02 6.41 9.20e-01 1.18e+00 4.86e+01 ... (remaining 39239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 16964 35.21 - 70.42: 418 70.42 - 105.63: 30 105.63 - 140.84: 8 140.84 - 176.05: 14 Dihedral angle restraints: 17434 sinusoidal: 7324 harmonic: 10110 Sorted by residual: dihedral pdb=" CA LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta harmonic sigma weight residual -180.00 -134.87 -45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA LYS C 506 " pdb=" C LYS C 506 " pdb=" N PRO C 507 " pdb=" CA PRO C 507 " ideal model delta harmonic sigma weight residual -180.00 -134.90 -45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA SER D 139 " pdb=" C SER D 139 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " ideal model delta harmonic sigma weight residual 180.00 141.40 38.60 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 17431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 4278 1.021 - 2.041: 2 2.041 - 3.062: 2 3.062 - 4.082: 0 4.082 - 5.103: 4 Chirality restraints: 4286 Sorted by residual: chirality pdb=" C17 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C16 CLR D1103 " pdb=" C20 CLR D1103 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C17 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C16 CLR B1103 " pdb=" C20 CLR B1103 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C9 CLR B1103 " pdb=" C10 CLR B1103 " pdb=" C11 CLR B1103 " pdb=" C8 CLR B1103 " both_signs ideal model delta sigma weight residual False -2.45 2.40 -4.85 2.00e-01 2.50e+01 5.88e+02 ... (remaining 4283 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.030 2.00e-02 2.50e+03 2.23e-02 1.12e+01 pdb=" C03 6ZP C1101 " 0.021 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.018 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.021 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.011 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " 0.001 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.010 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.030 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" C03 6ZP A1101 " -0.020 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.018 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.021 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.010 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " -0.002 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.010 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP B1101 " -0.029 2.00e-02 2.50e+03 2.15e-02 1.04e+01 pdb=" C03 6ZP B1101 " -0.018 2.00e-02 2.50e+03 pdb=" C04 6ZP B1101 " -0.014 2.00e-02 2.50e+03 pdb=" C05 6ZP B1101 " -0.002 2.00e-02 2.50e+03 pdb=" C06 6ZP B1101 " 0.016 2.00e-02 2.50e+03 pdb=" C07 6ZP B1101 " 0.019 2.00e-02 2.50e+03 pdb=" C08 6ZP B1101 " 0.003 2.00e-02 2.50e+03 pdb=" C09 6ZP B1101 " -0.017 2.00e-02 2.50e+03 pdb=" N01 6ZP B1101 " 0.043 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7167 2.78 - 3.31: 24857 3.31 - 3.84: 47050 3.84 - 4.37: 58931 4.37 - 4.90: 98822 Nonbonded interactions: 236827 Sorted by model distance: nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D1201 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN B 586 " pdb=" O HOH B1201 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 533 " pdb=" O LEU A 577 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR C 533 " pdb=" O LEU C 577 " model vdw 2.297 3.040 nonbonded pdb=" O VAL C 52 " pdb=" OG SER C 81 " model vdw 2.300 3.040 ... (remaining 236822 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 1034 or resid 1101 through 1106)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 3.580 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: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 75.250 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.016 0.535 29080 Z= 1.054 Angle : 1.433 24.538 39244 Z= 0.748 Chirality : 0.181 5.103 4286 Planarity : 0.007 0.075 4878 Dihedral : 15.641 176.051 10948 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.12 % Favored : 92.19 % Rotamer: Outliers : 1.33 % Allowed : 5.07 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.24 % 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: -4.85 (0.11), residues: 3482 helix: -3.66 (0.08), residues: 1648 sheet: -1.90 (0.23), residues: 422 loop : -2.85 (0.13), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP A 323 HIS 0.019 0.005 HIS A 219 PHE 0.037 0.005 PHE C 667 TYR 0.043 0.004 TYR D 702 ARG 0.014 0.002 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 447 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7776 (m-30) cc_final: 0.7491 (m-30) REVERT: A 121 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 143 LEU cc_start: 0.9054 (mm) cc_final: 0.8817 (mm) REVERT: A 187 LYS cc_start: 0.8300 (mttp) cc_final: 0.8084 (mttp) REVERT: A 197 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6250 (pm20) REVERT: A 222 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8481 (mt) REVERT: A 298 ASN cc_start: 0.5859 (m-40) cc_final: 0.5588 (m110) REVERT: A 585 MET cc_start: 0.6971 (mmt) cc_final: 0.6743 (mmm) REVERT: A 670 MET cc_start: 0.9149 (mtp) cc_final: 0.8868 (mtp) REVERT: A 864 LEU cc_start: 0.7091 (tt) cc_final: 0.6640 (tm) REVERT: A 883 HIS cc_start: 0.5424 (m90) cc_final: 0.4915 (m170) REVERT: A 1000 ASN cc_start: 0.6915 (m-40) cc_final: 0.6419 (t0) REVERT: A 1001 TYR cc_start: 0.7242 (p90) cc_final: 0.6782 (p90) REVERT: A 1029 MET cc_start: 0.4759 (mmm) cc_final: 0.3918 (tmm) REVERT: B 46 HIS cc_start: 0.7581 (t70) cc_final: 0.7248 (t70) REVERT: B 435 HIS cc_start: 0.7410 (m-70) cc_final: 0.7004 (t70) REVERT: B 441 LYS cc_start: 0.8048 (tppt) cc_final: 0.7838 (tptp) REVERT: B 511 LYS cc_start: 0.8475 (ptmt) cc_final: 0.8265 (mtmm) REVERT: B 613 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 719 ASP cc_start: 0.6760 (t0) cc_final: 0.6481 (t0) REVERT: B 752 LYS cc_start: 0.8235 (ttmp) cc_final: 0.8001 (ttpt) REVERT: C 71 TYR cc_start: 0.7859 (m-80) cc_final: 0.7565 (m-80) REVERT: C 298 ASN cc_start: 0.5402 (m-40) cc_final: 0.5070 (m110) REVERT: C 302 GLN cc_start: 0.7061 (tt0) cc_final: 0.6441 (pt0) REVERT: C 864 LEU cc_start: 0.7078 (tt) cc_final: 0.6745 (tm) REVERT: C 907 MET cc_start: 0.3096 (tpt) cc_final: 0.2820 (pmm) REVERT: C 980 TYR cc_start: 0.8257 (t80) cc_final: 0.8020 (t80) REVERT: C 988 MET cc_start: 0.7493 (mmm) cc_final: 0.6758 (mtm) REVERT: C 1000 ASN cc_start: 0.7023 (m-40) cc_final: 0.6723 (m-40) REVERT: D 266 GLU cc_start: 0.7618 (pm20) cc_final: 0.6623 (tt0) REVERT: D 293 THR cc_start: 0.7788 (m) cc_final: 0.7562 (p) REVERT: D 383 THR cc_start: 0.7779 (t) cc_final: 0.7391 (p) REVERT: D 435 HIS cc_start: 0.7582 (m-70) cc_final: 0.6984 (t70) REVERT: D 524 GLU cc_start: 0.7728 (mp0) cc_final: 0.7340 (mp0) REVERT: D 613 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8668 (mp) REVERT: D 752 LYS cc_start: 0.8271 (ttmp) cc_final: 0.7978 (ttpt) REVERT: D 798 ILE cc_start: 0.7804 (mt) cc_final: 0.7558 (mp) outliers start: 40 outliers final: 10 residues processed: 484 average time/residue: 1.4153 time to fit residues: 801.9403 Evaluate side-chains 283 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 317 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A 274 HIS A 318 ASN A 344 ASN A 569 ASN A 586 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A 747 ASN A 883 HIS A 947 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 46 HIS B 54 ASN B 164 ASN B 214 HIS B 318 ASN B 335 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 412 HIS B 508 GLN B 569 ASN B 747 ASN C 10 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 344 ASN C 569 ASN C 586 GLN C 726 ASN C 747 ASN C 947 ASN C 950 HIS ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN D 46 HIS D 54 ASN D 60 ASN D 164 ASN D 214 HIS D 224 ASN D 318 ASN D 335 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 412 HIS D 569 ASN D 747 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29080 Z= 0.215 Angle : 0.766 34.316 39244 Z= 0.374 Chirality : 0.057 1.719 4286 Planarity : 0.005 0.062 4878 Dihedral : 16.262 173.231 4490 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.34 % Favored : 94.20 % Rotamer: Outliers : 2.54 % Allowed : 9.94 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.12 % 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: -2.58 (0.13), residues: 3482 helix: -1.14 (0.11), residues: 1670 sheet: -1.50 (0.21), residues: 498 loop : -2.41 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 323 HIS 0.009 0.001 HIS D 93 PHE 0.020 0.002 PHE A 546 TYR 0.021 0.002 TYR C 673 ARG 0.011 0.001 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 324 time to evaluate : 3.116 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7517 (m-30) cc_final: 0.7241 (m-30) REVERT: A 187 LYS cc_start: 0.8423 (mttp) cc_final: 0.8196 (mtmp) REVERT: A 266 GLU cc_start: 0.7574 (pm20) cc_final: 0.6728 (tp30) REVERT: A 392 GLN cc_start: 0.6681 (mm-40) cc_final: 0.5359 (tm-30) REVERT: A 416 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: A 419 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: A 581 LEU cc_start: 0.7019 (tt) cc_final: 0.6585 (tm) REVERT: A 644 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6359 (pt0) REVERT: A 670 MET cc_start: 0.9045 (mtp) cc_final: 0.8773 (mtp) REVERT: A 864 LEU cc_start: 0.7021 (tt) cc_final: 0.6520 (tm) REVERT: A 883 HIS cc_start: 0.5044 (m-70) cc_final: 0.4768 (m170) REVERT: A 1000 ASN cc_start: 0.7235 (m-40) cc_final: 0.6619 (t0) REVERT: A 1001 TYR cc_start: 0.6759 (p90) cc_final: 0.6524 (p90) REVERT: A 1002 LYS cc_start: 0.6874 (tppp) cc_final: 0.6312 (tmtp) REVERT: B 293 THR cc_start: 0.7881 (m) cc_final: 0.7543 (p) REVERT: B 298 ASN cc_start: 0.7721 (t0) cc_final: 0.7430 (t0) REVERT: B 435 HIS cc_start: 0.7142 (m-70) cc_final: 0.6866 (t-90) REVERT: B 441 LYS cc_start: 0.7663 (tppt) cc_final: 0.7369 (tptm) REVERT: B 511 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8189 (mtmm) REVERT: B 527 MET cc_start: 0.6965 (mmm) cc_final: 0.6762 (mmm) REVERT: B 752 LYS cc_start: 0.8149 (ttmp) cc_final: 0.7918 (ttpm) REVERT: C 23 ASP cc_start: 0.7664 (m-30) cc_final: 0.7337 (m-30) REVERT: C 71 TYR cc_start: 0.7819 (m-80) cc_final: 0.7482 (m-80) REVERT: C 113 MET cc_start: 0.8313 (mmm) cc_final: 0.8025 (mmm) REVERT: C 268 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8281 (pmmt) REVERT: C 380 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7193 (ttt) REVERT: C 585 MET cc_start: 0.6591 (mmt) cc_final: 0.6252 (mmt) REVERT: C 863 TYR cc_start: 0.6752 (m-10) cc_final: 0.6441 (m-10) REVERT: C 864 LEU cc_start: 0.7003 (tt) cc_final: 0.6687 (tm) REVERT: C 907 MET cc_start: 0.2960 (tpt) cc_final: 0.2436 (pmm) REVERT: C 924 MET cc_start: 0.6492 (mmm) cc_final: 0.6103 (mpp) REVERT: C 980 TYR cc_start: 0.8037 (t80) cc_final: 0.7811 (t80) REVERT: C 987 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7029 (mm-30) REVERT: C 988 MET cc_start: 0.7462 (mmm) cc_final: 0.6776 (ttm) REVERT: C 1000 ASN cc_start: 0.7200 (m-40) cc_final: 0.6642 (t0) REVERT: C 1001 TYR cc_start: 0.7168 (p90) cc_final: 0.6032 (p90) REVERT: D 268 LYS cc_start: 0.8584 (tppt) cc_final: 0.7906 (mptp) REVERT: D 293 THR cc_start: 0.7649 (m) cc_final: 0.7413 (p) REVERT: D 294 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: D 300 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7763 (ttm110) REVERT: D 435 HIS cc_start: 0.7259 (m-70) cc_final: 0.6889 (t-90) REVERT: D 524 GLU cc_start: 0.7679 (mp0) cc_final: 0.7469 (mp0) REVERT: D 527 MET cc_start: 0.7129 (mmm) cc_final: 0.6844 (mpp) REVERT: D 719 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6055 (t0) REVERT: D 752 LYS cc_start: 0.8156 (ttmp) cc_final: 0.7883 (ttpm) outliers start: 76 outliers final: 26 residues processed: 379 average time/residue: 1.3058 time to fit residues: 586.6708 Evaluate side-chains 298 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 719 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 264 optimal weight: 0.0370 chunk 216 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 255 optimal weight: 20.0000 overall best weight: 0.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 337 GLN B 344 ASN B 709 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29080 Z= 0.186 Angle : 0.704 34.216 39244 Z= 0.334 Chirality : 0.055 1.653 4286 Planarity : 0.004 0.053 4878 Dihedral : 15.687 177.026 4481 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.92 % Favored : 93.83 % Rotamer: Outliers : 3.07 % Allowed : 11.54 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.06 % 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: -1.29 (0.14), residues: 3482 helix: 0.31 (0.12), residues: 1676 sheet: -1.34 (0.22), residues: 494 loop : -2.17 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 578 HIS 0.007 0.001 HIS D 93 PHE 0.016 0.001 PHE A1028 TYR 0.013 0.001 TYR A 77 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 295 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7537 (m-30) cc_final: 0.7287 (m-30) REVERT: A 266 GLU cc_start: 0.7532 (pm20) cc_final: 0.6753 (tp30) REVERT: A 360 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 416 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5595 (tp30) REVERT: A 864 LEU cc_start: 0.7025 (tt) cc_final: 0.6520 (tm) REVERT: A 1000 ASN cc_start: 0.7194 (m-40) cc_final: 0.6452 (t0) REVERT: A 1002 LYS cc_start: 0.6852 (tppp) cc_final: 0.6287 (tmtp) REVERT: B 42 ARG cc_start: 0.7123 (mmm-85) cc_final: 0.6487 (mpt-90) REVERT: B 50 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7815 (pp) REVERT: B 293 THR cc_start: 0.7847 (m) cc_final: 0.7489 (p) REVERT: B 435 HIS cc_start: 0.7077 (m-70) cc_final: 0.6761 (t-90) REVERT: B 441 LYS cc_start: 0.7638 (tppt) cc_final: 0.7420 (tptp) REVERT: B 511 LYS cc_start: 0.8422 (ptmt) cc_final: 0.8208 (mtmt) REVERT: B 527 MET cc_start: 0.6990 (mmm) cc_final: 0.6768 (mmm) REVERT: B 578 TRP cc_start: 0.7246 (t-100) cc_final: 0.6771 (t-100) REVERT: B 752 LYS cc_start: 0.8157 (ttmp) cc_final: 0.7942 (ttpm) REVERT: C 23 ASP cc_start: 0.7695 (m-30) cc_final: 0.7390 (m-30) REVERT: C 71 TYR cc_start: 0.7788 (m-80) cc_final: 0.7493 (m-80) REVERT: C 113 MET cc_start: 0.8294 (mmm) cc_final: 0.8014 (mmm) REVERT: C 268 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8335 (pmmt) REVERT: C 294 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6457 (tm-30) REVERT: C 585 MET cc_start: 0.6667 (mmt) cc_final: 0.6211 (mmm) REVERT: C 864 LEU cc_start: 0.7102 (tt) cc_final: 0.6676 (tm) REVERT: C 891 PHE cc_start: 0.6570 (m-80) cc_final: 0.6337 (m-80) REVERT: C 907 MET cc_start: 0.2854 (tpt) cc_final: 0.2444 (pmm) REVERT: C 987 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7056 (mm-30) REVERT: C 988 MET cc_start: 0.7491 (mmm) cc_final: 0.6996 (ttm) REVERT: C 999 PHE cc_start: 0.7193 (m-80) cc_final: 0.6779 (t80) REVERT: C 1000 ASN cc_start: 0.7273 (m-40) cc_final: 0.6692 (t0) REVERT: C 1001 TYR cc_start: 0.7083 (p90) cc_final: 0.6050 (p90) REVERT: C 1029 MET cc_start: 0.5972 (mmm) cc_final: 0.4828 (tmm) REVERT: D 266 GLU cc_start: 0.7557 (pm20) cc_final: 0.6613 (tt0) REVERT: D 293 THR cc_start: 0.7601 (m) cc_final: 0.7344 (p) REVERT: D 298 ASN cc_start: 0.7187 (m-40) cc_final: 0.6778 (m110) REVERT: D 300 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7736 (ttm170) REVERT: D 435 HIS cc_start: 0.7178 (m-70) cc_final: 0.6781 (t-90) REVERT: D 524 GLU cc_start: 0.7647 (mp0) cc_final: 0.7441 (mp0) REVERT: D 527 MET cc_start: 0.7132 (mmm) cc_final: 0.6769 (mpp) REVERT: D 752 LYS cc_start: 0.8198 (ttmp) cc_final: 0.7944 (ttpm) outliers start: 92 outliers final: 32 residues processed: 359 average time/residue: 1.2844 time to fit residues: 548.2068 Evaluate side-chains 300 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 265 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 0.8980 chunk 239 optimal weight: 0.0020 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 302 optimal weight: 0.0030 chunk 91 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 709 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29080 Z= 0.158 Angle : 0.677 34.075 39244 Z= 0.317 Chirality : 0.054 1.658 4286 Planarity : 0.004 0.050 4878 Dihedral : 15.343 176.068 4477 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 2.84 % Allowed : 12.61 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.06 % 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: -0.64 (0.14), residues: 3482 helix: 1.02 (0.13), residues: 1674 sheet: -1.32 (0.22), residues: 496 loop : -1.97 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 578 HIS 0.006 0.001 HIS D 93 PHE 0.022 0.001 PHE A 960 TYR 0.012 0.001 TYR D 469 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 280 time to evaluate : 3.225 Fit side-chains revert: symmetry clash REVERT: A 111 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 187 LYS cc_start: 0.8174 (mtmp) cc_final: 0.7869 (ptpp) REVERT: A 203 ASP cc_start: 0.6916 (m-30) cc_final: 0.6710 (m-30) REVERT: A 257 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7764 (mttp) REVERT: A 266 GLU cc_start: 0.7504 (pm20) cc_final: 0.6753 (tp30) REVERT: A 360 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 392 GLN cc_start: 0.6787 (mm-40) cc_final: 0.5409 (mm-40) REVERT: A 393 LYS cc_start: 0.7867 (tptt) cc_final: 0.7448 (ttpt) REVERT: A 416 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5547 (tp30) REVERT: A 431 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 594 ARG cc_start: 0.6638 (mmp-170) cc_final: 0.6408 (mmm160) REVERT: A 807 MET cc_start: 0.7128 (mmp) cc_final: 0.6898 (mmp) REVERT: A 864 LEU cc_start: 0.6991 (tt) cc_final: 0.6515 (tm) REVERT: A 1000 ASN cc_start: 0.7184 (m-40) cc_final: 0.6375 (t0) REVERT: A 1002 LYS cc_start: 0.6884 (tppp) cc_final: 0.6284 (tmtp) REVERT: B 42 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.6484 (mpt-90) REVERT: B 293 THR cc_start: 0.7820 (m) cc_final: 0.7463 (p) REVERT: B 435 HIS cc_start: 0.6995 (m-70) cc_final: 0.6680 (t-90) REVERT: B 441 LYS cc_start: 0.7593 (tppt) cc_final: 0.7386 (tptp) REVERT: B 511 LYS cc_start: 0.8406 (ptmt) cc_final: 0.8182 (mtmm) REVERT: B 527 MET cc_start: 0.6986 (mmm) cc_final: 0.6747 (mmm) REVERT: B 578 TRP cc_start: 0.7230 (t-100) cc_final: 0.6694 (t-100) REVERT: B 752 LYS cc_start: 0.8149 (ttmp) cc_final: 0.7917 (ttpm) REVERT: C 23 ASP cc_start: 0.7643 (m-30) cc_final: 0.7371 (m-30) REVERT: C 113 MET cc_start: 0.8284 (mmm) cc_final: 0.7992 (mmm) REVERT: C 187 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (ptpp) REVERT: C 268 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8339 (pmmt) REVERT: C 294 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6546 (tm-30) REVERT: C 431 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 585 MET cc_start: 0.6677 (mmt) cc_final: 0.6442 (mmm) REVERT: C 864 LEU cc_start: 0.7156 (tt) cc_final: 0.6700 (tm) REVERT: C 924 MET cc_start: 0.6549 (mmm) cc_final: 0.6098 (mpp) REVERT: C 987 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7137 (mm-30) REVERT: C 988 MET cc_start: 0.7374 (mmm) cc_final: 0.6810 (ttm) REVERT: C 1000 ASN cc_start: 0.7224 (m-40) cc_final: 0.6698 (t0) REVERT: C 1001 TYR cc_start: 0.7060 (p90) cc_final: 0.5914 (p90) REVERT: C 1029 MET cc_start: 0.5734 (mmm) cc_final: 0.4579 (tmm) REVERT: D 12 ILE cc_start: 0.7983 (mt) cc_final: 0.7775 (tt) REVERT: D 50 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (pp) REVERT: D 266 GLU cc_start: 0.7553 (pm20) cc_final: 0.6806 (tt0) REVERT: D 293 THR cc_start: 0.7539 (m) cc_final: 0.7277 (p) REVERT: D 298 ASN cc_start: 0.7186 (m-40) cc_final: 0.6762 (m110) REVERT: D 393 LYS cc_start: 0.7570 (tttm) cc_final: 0.7205 (tptm) REVERT: D 435 HIS cc_start: 0.7093 (m-70) cc_final: 0.6719 (t-90) REVERT: D 524 GLU cc_start: 0.7552 (mp0) cc_final: 0.7307 (mp0) REVERT: D 527 MET cc_start: 0.7068 (mmm) cc_final: 0.6743 (mpp) REVERT: D 752 LYS cc_start: 0.8186 (ttmp) cc_final: 0.7919 (ttpm) outliers start: 85 outliers final: 36 residues processed: 338 average time/residue: 1.2443 time to fit residues: 494.7301 Evaluate side-chains 302 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 800 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 233 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 172 optimal weight: 0.0060 chunk 303 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 337 GLN B 412 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 709 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29080 Z= 0.169 Angle : 0.675 33.959 39244 Z= 0.314 Chirality : 0.054 1.658 4286 Planarity : 0.004 0.050 4878 Dihedral : 15.142 176.040 4477 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.80 % Favored : 94.08 % Rotamer: Outliers : 2.90 % Allowed : 13.01 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.06 % 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: -0.33 (0.15), residues: 3482 helix: 1.32 (0.13), residues: 1682 sheet: -1.26 (0.22), residues: 500 loop : -1.87 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 578 HIS 0.006 0.001 HIS D 93 PHE 0.016 0.001 PHE C1028 TYR 0.013 0.001 TYR D 469 ARG 0.005 0.000 ARG A 834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 266 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8144 (mtmp) cc_final: 0.7857 (ptpp) REVERT: A 266 GLU cc_start: 0.7523 (pm20) cc_final: 0.6773 (tp30) REVERT: A 393 LYS cc_start: 0.7886 (tptt) cc_final: 0.7537 (ttpt) REVERT: A 431 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 807 MET cc_start: 0.7169 (mmp) cc_final: 0.6944 (mmp) REVERT: A 864 LEU cc_start: 0.6998 (tt) cc_final: 0.6485 (tm) REVERT: A 987 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6949 (mm-30) REVERT: A 1000 ASN cc_start: 0.7211 (m-40) cc_final: 0.6299 (t0) REVERT: A 1002 LYS cc_start: 0.6930 (tppp) cc_final: 0.6307 (tmtp) REVERT: B 42 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6558 (mpt-90) REVERT: B 293 THR cc_start: 0.7843 (m) cc_final: 0.7485 (p) REVERT: B 435 HIS cc_start: 0.6987 (m-70) cc_final: 0.6726 (t70) REVERT: B 441 LYS cc_start: 0.7607 (tppt) cc_final: 0.7374 (tptp) REVERT: B 511 LYS cc_start: 0.8368 (ptmt) cc_final: 0.8132 (mtmm) REVERT: B 527 MET cc_start: 0.7023 (mmm) cc_final: 0.6768 (mmm) REVERT: B 578 TRP cc_start: 0.7216 (t-100) cc_final: 0.6742 (t-100) REVERT: B 752 LYS cc_start: 0.8156 (ttmp) cc_final: 0.7908 (ttpm) REVERT: C 23 ASP cc_start: 0.7662 (m-30) cc_final: 0.7396 (m-30) REVERT: C 113 MET cc_start: 0.8269 (mmm) cc_final: 0.7979 (mmm) REVERT: C 187 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (ptpp) REVERT: C 268 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8332 (pmmt) REVERT: C 294 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6417 (tm-30) REVERT: C 416 GLU cc_start: 0.6364 (mm-30) cc_final: 0.6124 (mp0) REVERT: C 431 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 864 LEU cc_start: 0.7172 (tt) cc_final: 0.6705 (tm) REVERT: C 907 MET cc_start: 0.2880 (tmt) cc_final: 0.2302 (ptm) REVERT: C 924 MET cc_start: 0.6531 (mmm) cc_final: 0.6114 (mpp) REVERT: C 972 SER cc_start: 0.6970 (m) cc_final: 0.6413 (p) REVERT: C 987 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 988 MET cc_start: 0.7404 (mmm) cc_final: 0.6994 (ttm) REVERT: C 999 PHE cc_start: 0.7567 (m-80) cc_final: 0.7106 (t80) REVERT: C 1000 ASN cc_start: 0.7197 (m-40) cc_final: 0.6663 (t0) REVERT: C 1001 TYR cc_start: 0.7142 (p90) cc_final: 0.5970 (p90) REVERT: C 1002 LYS cc_start: 0.6465 (tppp) cc_final: 0.5931 (tmtp) REVERT: C 1029 MET cc_start: 0.5565 (mmm) cc_final: 0.4454 (tmm) REVERT: D 12 ILE cc_start: 0.8046 (mt) cc_final: 0.7842 (tt) REVERT: D 50 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8006 (pp) REVERT: D 268 LYS cc_start: 0.8601 (tppt) cc_final: 0.7949 (mptp) REVERT: D 293 THR cc_start: 0.7554 (m) cc_final: 0.7274 (p) REVERT: D 294 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: D 298 ASN cc_start: 0.7111 (m-40) cc_final: 0.6702 (m110) REVERT: D 435 HIS cc_start: 0.7078 (m-70) cc_final: 0.6732 (t70) REVERT: D 524 GLU cc_start: 0.7470 (mp0) cc_final: 0.7228 (mp0) REVERT: D 527 MET cc_start: 0.7063 (mmm) cc_final: 0.6737 (mpp) REVERT: D 752 LYS cc_start: 0.8182 (ttmp) cc_final: 0.7897 (ttpm) outliers start: 87 outliers final: 43 residues processed: 331 average time/residue: 1.1116 time to fit residues: 436.9598 Evaluate side-chains 304 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 800 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 6.9990 chunk 304 optimal weight: 0.0030 chunk 66 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: