Starting phenix.real_space_refine on Sat Mar 7 05:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bqt_30155/03_2026/7bqt_30155.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 25116 2.51 5 N 6660 2.21 5 O 7248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 310 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 7.75, per 1000 atoms: 0.20 Number of scatterers: 39180 At special positions: 0 Unit cell: (151.96, 151.96, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 7248 8.00 N 6660 7.00 C 25116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 64 sheets defined 55.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 44 through 50 removed outlier: 4.011A pdb=" N ALA A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.753A pdb=" N HIS A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.970A pdb=" N VAL A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 131 removed outlier: 4.498A pdb=" N ARG A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.160A pdb=" N ASP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 4.113A pdb=" N SER A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 204 removed outlier: 4.768A pdb=" N THR A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.790A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 496 removed outlier: 3.773A pdb=" N LEU A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.780A pdb=" N GLY A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.840A pdb=" N TYR A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.760A pdb=" N ALA A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.591A pdb=" N SER A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.722A pdb=" N ILE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.927A pdb=" N ASN B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 71 removed outlier: 4.128A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.910A pdb=" N VAL B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 131 removed outlier: 4.239A pdb=" N LEU B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.843A pdb=" N ASP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TRP B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 4.174A pdb=" N SER B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 204 removed outlier: 4.961A pdb=" N THR B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 Processing helix chain 'B' and resid 439 through 449 removed outlier: 3.621A pdb=" N GLU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 496 removed outlier: 3.705A pdb=" N LEU B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 530 removed outlier: 3.958A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.530A pdb=" N TYR B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.660A pdb=" N ALA B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.954A pdb=" N ASN C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 removed outlier: 3.539A pdb=" N GLN C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.069A pdb=" N VAL C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 131 removed outlier: 3.774A pdb=" N LEU C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 4.110A pdb=" N ASP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 145 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 4.153A pdb=" N SER C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 204 removed outlier: 4.757A pdb=" N THR C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 278 Processing helix chain 'C' and resid 439 through 449 removed outlier: 3.524A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 496 removed outlier: 3.741A pdb=" N LEU C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 529 removed outlier: 3.844A pdb=" N ILE C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.628A pdb=" N TYR C 528 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.978A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.987A pdb=" N HIS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.838A pdb=" N VAL D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 131 removed outlier: 3.992A pdb=" N LEU D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.778A pdb=" N ASP D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 181 through 204 removed outlier: 4.959A pdb=" N THR D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 196 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 Processing helix chain 'D' and resid 439 through 449 removed outlier: 3.573A pdb=" N GLU D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 496 removed outlier: 3.722A pdb=" N LEU D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 529 removed outlier: 4.006A pdb=" N GLY D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.529A pdb=" N TYR D 528 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.511A pdb=" N ALA D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.892A pdb=" N ILE E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 50 removed outlier: 3.613A pdb=" N ALA E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.705A pdb=" N HIS E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 90 removed outlier: 4.216A pdb=" N VAL E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 131 removed outlier: 3.846A pdb=" N LEU E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.957A pdb=" N ASP E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 removed outlier: 3.747A pdb=" N SER E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 removed outlier: 4.008A pdb=" N THR E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 278 Processing helix chain 'E' and resid 439 through 449 removed outlier: 3.737A pdb=" N LEU E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 496 removed outlier: 3.803A pdb=" N LEU E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 487 " --> pdb=" O LYS E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 529 removed outlier: 4.042A pdb=" N ILE E 519 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.555A pdb=" N TYR E 528 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 546 removed outlier: 3.745A pdb=" N ALA E 544 " --> pdb=" O THR E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 558 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.955A pdb=" N ILE G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 removed outlier: 3.905A pdb=" N ALA G 48 " --> pdb=" O GLN G 44 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 71 removed outlier: 3.715A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 90 removed outlier: 4.105A pdb=" N VAL G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS G 79 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 131 removed outlier: 4.501A pdb=" N LEU G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.800A pdb=" N ASP G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 removed outlier: 3.966A pdb=" N SER G 164 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 204 removed outlier: 4.479A pdb=" N THR G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 278 Processing helix chain 'G' and resid 439 through 449 removed outlier: 3.525A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 496 removed outlier: 3.690A pdb=" N LEU G 485 " --> pdb=" O MET G 481 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU G 487 " --> pdb=" O LYS G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 529 removed outlier: 4.137A pdb=" N ILE G 519 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 520 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY G 524 " --> pdb=" O SER G 520 " (cutoff:3.500A) Proline residue: G 525 - end of helix Processing helix chain 'G' and resid 540 through 546 removed outlier: 3.782A pdb=" N ALA G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 558 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'I' and resid 24 through 33 removed outlier: 3.888A pdb=" N ILE I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 51 removed outlier: 3.968A pdb=" N ALA I 48 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 50 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 71 removed outlier: 3.824A pdb=" N HIS I 71 " --> pdb=" O ARG I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 90 removed outlier: 4.110A pdb=" N VAL I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 78 " --> pdb=" O TYR I 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS I 79 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 131 removed outlier: 4.311A pdb=" N LEU I 121 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.858A pdb=" N ASP I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR I 148 " --> pdb=" O TRP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 166 removed outlier: 3.705A pdb=" N SER I 164 " --> pdb=" O GLN I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 204 removed outlier: 4.010A pdb=" N THR I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 278 Processing helix chain 'I' and resid 439 through 449 removed outlier: 3.717A pdb=" N LEU I 447 " --> pdb=" O ALA I 443 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 496 removed outlier: 3.738A pdb=" N LEU I 485 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU I 487 " --> pdb=" O LYS I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 530 removed outlier: 4.127A pdb=" N ILE I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER I 520 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 524 " --> pdb=" O SER I 520 " (cutoff:3.500A) Proline residue: I 525 - end of helix removed outlier: 3.584A pdb=" N VAL I 530 " --> pdb=" O PHE I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 546 removed outlier: 3.642A pdb=" N ALA I 544 " --> pdb=" O THR I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 558 removed outlier: 4.077A pdb=" N ASP I 553 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 554 " --> pdb=" O GLU I 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER I 558 " --> pdb=" O GLU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 570 removed outlier: 3.615A pdb=" N ARG I 570 " --> pdb=" O GLU I 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 33 removed outlier: 3.931A pdb=" N ILE K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 50 removed outlier: 4.018A pdb=" N TYR K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU K 50 " --> pdb=" O ILE K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.725A pdb=" N HIS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 removed outlier: 4.143A pdb=" N VAL K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU K 78 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 131 removed outlier: 4.483A pdb=" N LEU K 121 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 removed outlier: 3.795A pdb=" N ASP K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP K 144 " --> pdb=" O ARG K 140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 166 removed outlier: 3.908A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 204 removed outlier: 4.365A pdb=" N THR K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS K 196 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU K 200 " --> pdb=" O LYS K 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 278 Processing helix chain 'K' and resid 439 through 449 removed outlier: 3.873A pdb=" N LEU K 447 " --> pdb=" O ALA K 443 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 477 through 496 removed outlier: 3.660A pdb=" N LEU K 485 " --> pdb=" O MET K 481 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU K 487 " --> pdb=" O LYS K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 530 removed outlier: 4.083A pdb=" N ILE K 519 " --> pdb=" O SER K 515 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER K 520 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 524 " --> pdb=" O SER K 520 " (cutoff:3.500A) Proline residue: K 525 - end of helix removed outlier: 3.648A pdb=" N TYR K 528 " --> pdb=" O GLY K 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 530 " --> pdb=" O PHE K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 546 removed outlier: 3.596A pdb=" N ALA K 544 " --> pdb=" O THR K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 558 Processing helix chain 'K' and resid 559 through 570 Processing helix chain 'F' and resid 24 through 33 removed outlier: 3.942A pdb=" N ILE F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 44 through 50 removed outlier: 3.851A pdb=" N ALA F 48 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 44 through 50' Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.880A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 90 removed outlier: 3.902A pdb=" N VAL F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 131 removed outlier: 4.097A pdb=" N LEU F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 146 removed outlier: 4.202A pdb=" N ASP F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 145 " --> pdb=" O TYR F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 166 Processing helix chain 'F' and resid 181 through 204 removed outlier: 3.514A pdb=" N ARG F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 278 Processing helix chain 'F' and resid 439 through 449 removed outlier: 3.824A pdb=" N LEU F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 496 removed outlier: 3.729A pdb=" N LEU F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 487 " --> pdb=" O LYS F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 529 removed outlier: 3.970A pdb=" N ILE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY F 524 " --> pdb=" O SER F 520 " (cutoff:3.500A) Proline residue: F 525 - end of helix removed outlier: 3.551A pdb=" N TYR F 528 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 546 removed outlier: 3.737A pdb=" N ALA F 544 " --> pdb=" O THR F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 557 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.023A pdb=" N ILE H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 44 through 51 removed outlier: 4.019A pdb=" N ALA H 48 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 removed outlier: 3.924A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 90 removed outlier: 3.970A pdb=" N HIS H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 131 removed outlier: 4.171A pdb=" N LEU H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 148 removed outlier: 4.065A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 145 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 181 through 204 removed outlier: 4.756A pdb=" N THR H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 196 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER H 201 " --> pdb=" O GLU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 278 Processing helix chain 'H' and resid 439 through 449 removed outlier: 3.847A pdb=" N LEU H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 496 removed outlier: 3.515A pdb=" N ASP H 484 " --> pdb=" O GLU H 480 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU H 485 " --> pdb=" O MET H 481 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU H 487 " --> pdb=" O LYS H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 529 removed outlier: 4.066A pdb=" N ILE H 519 " --> pdb=" O SER H 515 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER H 520 " --> pdb=" O SER H 516 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY H 524 " --> pdb=" O SER H 520 " (cutoff:3.500A) Proline residue: H 525 - end of helix removed outlier: 3.739A pdb=" N TYR H 528 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 546 removed outlier: 3.718A pdb=" N ALA H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 557 Processing helix chain 'H' and resid 559 through 568 Processing helix chain 'J' and resid 24 through 33 removed outlier: 3.955A pdb=" N ILE J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 4.178A pdb=" N TYR J 47 " --> pdb=" O GLY J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 90 removed outlier: 3.876A pdb=" N VAL J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 131 removed outlier: 4.275A pdb=" N LEU J 121 " --> pdb=" O THR J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 148 removed outlier: 3.865A pdb=" N ASP J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TRP J 144 " --> pdb=" O ARG J 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 145 " --> pdb=" O TYR J 141 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS J 146 " --> pdb=" O VAL J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 181 through 204 removed outlier: 4.592A pdb=" N THR J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS J 196 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU J 200 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 257 through 278 Processing helix chain 'J' and resid 439 through 449 removed outlier: 3.810A pdb=" N LEU J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 477 through 496 removed outlier: 3.780A pdb=" N LEU J 485 " --> pdb=" O MET J 481 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU J 487 " --> pdb=" O LYS J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 529 removed outlier: 3.890A pdb=" N ILE J 519 " --> pdb=" O SER J 515 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER J 520 " --> pdb=" O SER J 516 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY J 524 " --> pdb=" O SER J 520 " (cutoff:3.500A) Proline residue: J 525 - end of helix removed outlier: 3.743A pdb=" N TYR J 528 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 546 removed outlier: 3.657A pdb=" N ALA J 544 " --> pdb=" O THR J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 557 Processing helix chain 'J' and resid 559 through 568 Processing helix chain 'L' and resid 24 through 33 removed outlier: 3.905A pdb=" N ILE L 33 " --> pdb=" O ARG L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 44 through 50 removed outlier: 3.666A pdb=" N ALA L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 71 removed outlier: 3.706A pdb=" N HIS L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 90 removed outlier: 3.869A pdb=" N VAL L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 131 removed outlier: 4.067A pdb=" N LEU L 121 " --> pdb=" O THR L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 removed outlier: 3.700A pdb=" N ASP L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP L 144 " --> pdb=" O ARG L 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 145 " --> pdb=" O TYR L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 166 Processing helix chain 'L' and resid 181 through 204 removed outlier: 4.219A pdb=" N THR L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 196 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU L 200 " --> pdb=" O LYS L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 278 Processing helix chain 'L' and resid 439 through 449 removed outlier: 3.818A pdb=" N LEU L 447 " --> pdb=" O ALA L 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN L 449 " --> pdb=" O GLU L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 477 through 496 removed outlier: 3.682A pdb=" N LEU L 485 " --> pdb=" O MET L 481 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU L 487 " --> pdb=" O LYS L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 529 removed outlier: 4.034A pdb=" N ILE L 519 " --> pdb=" O SER L 515 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER L 520 " --> pdb=" O SER L 516 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY L 524 " --> pdb=" O SER L 520 " (cutoff:3.500A) Proline residue: L 525 - end of helix removed outlier: 3.598A pdb=" N TYR L 528 " --> pdb=" O GLY L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 546 removed outlier: 3.754A pdb=" N ALA L 544 " --> pdb=" O THR L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 557 Processing helix chain 'L' and resid 559 through 568 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.517A pdb=" N THR A 214 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.727A pdb=" N VAL A 151 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 236 " --> pdb=" O VAL A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.591A pdb=" N VAL A 154 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.724A pdb=" N ALA A 457 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 284 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN F 468 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 287 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE F 466 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 465 through 469 removed outlier: 7.086A pdb=" N ILE K 285 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.507A pdb=" N THR A 500 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 513 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.624A pdb=" N GLU B 223 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 206 removed outlier: 3.622A pdb=" N VAL B 151 " --> pdb=" O HIS B 236 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB2, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.671A pdb=" N ALA B 457 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 284 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 285 " --> pdb=" O ASN H 468 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN H 468 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 287 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE H 466 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 469 removed outlier: 3.854A pdb=" N SER B 465 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 285 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA E 284 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 499 through 502 removed outlier: 3.766A pdb=" N ARG B 513 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.679A pdb=" N GLU C 223 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 226 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 228 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 231 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 150 through 152 removed outlier: 3.627A pdb=" N VAL C 151 " --> pdb=" O HIS C 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB9, first strand: chain 'C' and resid 456 through 457 removed outlier: 4.569A pdb=" N ASN J 468 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY C 287 " --> pdb=" O ILE J 466 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE J 466 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 465 through 469 removed outlier: 3.503A pdb=" N SER C 465 " --> pdb=" O GLY G 287 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE G 285 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA G 284 " --> pdb=" O ALA G 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 499 through 502 removed outlier: 3.570A pdb=" N THR C 500 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 513 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.849A pdb=" N GLU D 223 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 226 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 228 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 231 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.612A pdb=" N VAL D 151 " --> pdb=" O HIS D 236 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC7, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.037A pdb=" N ALA D 284 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE D 285 " --> pdb=" O LEU L 467 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER L 465 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 465 through 469 removed outlier: 7.063A pdb=" N ILE I 285 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA I 284 " --> pdb=" O ALA I 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 499 through 502 removed outlier: 3.858A pdb=" N ARG D 513 " --> pdb=" O THR D 500 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.893A pdb=" N GLU E 223 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA E 226 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 228 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 231 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.537A pdb=" N VAL E 154 " --> pdb=" O PHE E 206 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'E' and resid 465 through 471 removed outlier: 6.140A pdb=" N ILE E 466 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY F 287 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN E 468 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 285 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA F 457 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 284 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 499 through 502 removed outlier: 3.711A pdb=" N ARG E 513 " --> pdb=" O THR E 500 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.720A pdb=" N GLU G 223 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 150 through 152 removed outlier: 3.897A pdb=" N VAL G 151 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS G 236 " --> pdb=" O VAL G 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE1, first strand: chain 'G' and resid 465 through 471 removed outlier: 6.193A pdb=" N ILE G 466 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY H 287 " --> pdb=" O ILE G 466 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN G 468 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 499 through 502 removed outlier: 3.792A pdb=" N ARG G 513 " --> pdb=" O THR G 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.801A pdb=" N GLU I 223 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA I 226 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR I 228 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG I 231 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 150 through 152 removed outlier: 3.681A pdb=" N VAL I 151 " --> pdb=" O HIS I 236 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AE6, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AE7, first strand: chain 'I' and resid 465 through 469 removed outlier: 4.249A pdb=" N SER I 465 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE J 285 " --> pdb=" O LEU I 467 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 499 through 502 removed outlier: 3.732A pdb=" N ARG I 513 " --> pdb=" O THR I 500 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.554A pdb=" N TYR K 217 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU K 223 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.717A pdb=" N VAL K 151 " --> pdb=" O HIS K 236 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 154 through 155 Processing sheet with id=AF3, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AF4, first strand: chain 'K' and resid 465 through 471 removed outlier: 6.051A pdb=" N ILE K 466 " --> pdb=" O GLY L 287 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY L 287 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN K 468 " --> pdb=" O ILE L 285 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA L 457 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA L 284 " --> pdb=" O ALA L 457 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 499 through 502 removed outlier: 3.718A pdb=" N ARG K 513 " --> pdb=" O THR K 500 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.657A pdb=" N TYR F 217 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU F 223 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR F 224 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 235 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 226 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR F 228 " --> pdb=" O ARG F 231 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 231 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N ARG F 232 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS F 155 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 151 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AF8, first strand: chain 'F' and resid 499 through 502 removed outlier: 3.701A pdb=" N ARG F 513 " --> pdb=" O THR F 500 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 20 removed outlier: 8.434A pdb=" N TYR H 224 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU H 235 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA H 226 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR H 228 " --> pdb=" O ARG H 231 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG H 231 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N ARG H 232 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LYS H 155 " --> pdb=" O ARG H 232 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS H 236 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 151 " --> pdb=" O HIS H 236 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AG2, first strand: chain 'H' and resid 499 through 502 removed outlier: 3.683A pdb=" N ARG H 513 " --> pdb=" O THR H 500 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 19 through 20 removed outlier: 3.703A pdb=" N TYR J 217 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU J 223 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N TYR J 224 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU J 235 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 231 " --> pdb=" O TYR J 228 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ARG J 232 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS J 155 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS J 236 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL J 151 " --> pdb=" O HIS J 236 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 242 through 243 Processing sheet with id=AG5, first strand: chain 'J' and resid 499 through 502 removed outlier: 3.689A pdb=" N ARG J 513 " --> pdb=" O THR J 500 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.643A pdb=" N TYR L 217 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU L 223 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA L 226 " --> pdb=" O ILE L 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR L 228 " --> pdb=" O ARG L 231 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 231 " --> pdb=" O TYR L 228 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 150 through 152 removed outlier: 3.582A pdb=" N VAL L 151 " --> pdb=" O HIS L 236 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AG9, first strand: chain 'L' and resid 242 through 243 Processing sheet with id=AH1, first strand: chain 'L' and resid 499 through 502 removed outlier: 3.839A pdb=" N ARG L 513 " --> pdb=" O THR L 500 " (cutoff:3.500A) 1822 hydrogen bonds defined for protein. 5286 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: 7.50 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12028 1.34 - 1.46: 8228 1.46 - 1.58: 19608 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 40068 Sorted by residual: bond pdb=" C HIS C 22 " pdb=" N PRO C 23 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.61e+01 bond pdb=" C HIS B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 1.334 1.362 -0.029 8.40e-03 1.42e+04 1.17e+01 bond pdb=" C HIS E 22 " pdb=" N PRO E 23 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" CA LEU C 218 " pdb=" CB LEU C 218 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.55e-02 4.16e+03 4.52e+00 bond pdb=" CB THR K 279 " pdb=" CG2 THR K 279 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 ... (remaining 40063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 52898 2.66 - 5.32: 1316 5.32 - 7.99: 136 7.99 - 10.65: 70 10.65 - 13.31: 12 Bond angle restraints: 54432 Sorted by residual: angle pdb=" C VAL K 60 " pdb=" N PHE K 61 " pdb=" CA PHE K 61 " ideal model delta sigma weight residual 120.65 126.20 -5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" C SER L 168 " pdb=" N LEU L 169 " pdb=" CA LEU L 169 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C SER G 168 " pdb=" N LEU G 169 " pdb=" CA LEU G 169 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER E 168 " pdb=" N LEU E 169 " pdb=" CA LEU E 169 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C VAL A 60 " pdb=" N PHE A 61 " pdb=" CA PHE A 61 " ideal model delta sigma weight residual 120.65 125.71 -5.06 1.32e+00 5.74e-01 1.47e+01 ... (remaining 54427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 21051 17.95 - 35.90: 2446 35.90 - 53.86: 422 53.86 - 71.81: 65 71.81 - 89.76: 64 Dihedral angle restraints: 24048 sinusoidal: 9636 harmonic: 14412 Sorted by residual: dihedral pdb=" CA LEU I 257 " pdb=" C LEU I 257 " pdb=" N TYR I 258 " pdb=" CA TYR I 258 " ideal model delta harmonic sigma weight residual 180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU G 257 " pdb=" C LEU G 257 " pdb=" N TYR G 258 " pdb=" CA TYR G 258 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 257 " pdb=" C LEU A 257 " pdb=" N TYR A 258 " pdb=" CA TYR A 258 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 24045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5275 0.082 - 0.164: 889 0.164 - 0.246: 79 0.246 - 0.328: 19 0.328 - 0.410: 2 Chirality restraints: 6264 Sorted by residual: chirality pdb=" CG LEU F 122 " pdb=" CB LEU F 122 " pdb=" CD1 LEU F 122 " pdb=" CD2 LEU F 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE E 166 " pdb=" CA ILE E 166 " pdb=" CG1 ILE E 166 " pdb=" CG2 ILE E 166 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE G 215 " pdb=" CA ILE G 215 " pdb=" CG1 ILE G 215 " pdb=" CG2 ILE G 215 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 6261 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 118 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C VAL G 118 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL G 118 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG G 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 63 " 0.019 2.00e-02 2.50e+03 2.45e-02 8.97e+00 pdb=" CG HIS K 63 " -0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS K 63 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS K 63 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS K 63 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS K 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 63 " 0.019 2.00e-02 2.50e+03 2.40e-02 8.61e+00 pdb=" CG HIS B 63 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS B 63 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS B 63 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS B 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 63 " 0.002 2.00e-02 2.50e+03 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7804 2.76 - 3.30: 40238 3.30 - 3.83: 69666 3.83 - 4.37: 78009 4.37 - 4.90: 125205 Nonbonded interactions: 320922 Sorted by model distance: nonbonded pdb=" OH TYR J 528 " pdb=" O VAL J 536 " model vdw 2.230 3.040 nonbonded pdb=" O LYS B 483 " pdb=" OG1 THR B 486 " model vdw 2.232 3.040 nonbonded pdb=" O LYS G 483 " pdb=" OG1 THR G 486 " model vdw 2.239 3.040 nonbonded pdb=" O LYS L 483 " pdb=" OG1 THR L 486 " model vdw 2.242 3.040 nonbonded pdb=" O ARG B 119 " pdb=" OG1 THR B 123 " model vdw 2.246 3.040 ... (remaining 320917 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 32.530 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.006 0.063 40068 Z= 0.283 Angle : 1.070 13.311 54432 Z= 0.580 Chirality : 0.061 0.410 6264 Planarity : 0.007 0.064 6840 Dihedral : 15.962 89.761 14712 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.66 % Allowed : 13.93 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.10), residues: 4788 helix: -2.82 (0.08), residues: 2280 sheet: -2.28 (0.31), residues: 264 loop : -2.67 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 140 TYR 0.030 0.002 TYR F 138 PHE 0.048 0.003 PHE K 61 TRP 0.019 0.002 TRP B 144 HIS 0.030 0.002 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00579 (40068) covalent geometry : angle 1.07026 (54432) hydrogen bonds : bond 0.20188 ( 1822) hydrogen bonds : angle 8.20254 ( 5286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8933 (t0) cc_final: 0.8711 (m110) REVERT: A 61 PHE cc_start: 0.9066 (t80) cc_final: 0.8761 (t80) REVERT: A 74 TYR cc_start: 0.8771 (t80) cc_final: 0.8409 (p90) REVERT: A 75 ASP cc_start: 0.9282 (t0) cc_final: 0.8974 (t0) REVERT: A 81 TRP cc_start: 0.8368 (t60) cc_final: 0.8121 (t60) REVERT: A 83 LYS cc_start: 0.9234 (mptt) cc_final: 0.8734 (mmtm) REVERT: A 87 CYS cc_start: 0.9203 (t) cc_final: 0.8836 (m) REVERT: A 103 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8791 (mmt-90) REVERT: A 131 HIS cc_start: 0.8981 (m-70) cc_final: 0.8678 (m-70) REVERT: A 182 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8463 (mmm-85) REVERT: A 185 ARG cc_start: 0.8725 (mmt180) cc_final: 0.8337 (ttp80) REVERT: A 193 GLU cc_start: 0.9586 (pp20) cc_final: 0.9094 (pp20) REVERT: A 197 GLU cc_start: 0.9399 (mp0) cc_final: 0.9113 (mp0) REVERT: A 224 TYR cc_start: 0.8745 (m-80) cc_final: 0.8354 (m-80) REVERT: A 234 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7956 (ttp80) REVERT: A 259 GLN cc_start: 0.9193 (pm20) cc_final: 0.8853 (pm20) REVERT: A 263 MET cc_start: 0.9061 (tmm) cc_final: 0.8819 (tmm) REVERT: A 444 ILE cc_start: 0.9447 (mm) cc_final: 0.9236 (mm) REVERT: A 448 PHE cc_start: 0.8508 (m-80) cc_final: 0.8265 (m-80) REVERT: A 474 TYR cc_start: 0.8939 (t80) cc_final: 0.8717 (t80) REVERT: A 479 ARG cc_start: 0.8763 (ptm-80) cc_final: 0.8367 (ptm-80) REVERT: A 483 LYS cc_start: 0.9316 (tppp) cc_final: 0.8864 (tmtt) REVERT: A 490 GLU cc_start: 0.8861 (tt0) cc_final: 0.8037 (tt0) REVERT: A 492 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 493 LEU cc_start: 0.9463 (mt) cc_final: 0.8961 (mt) REVERT: A 494 PHE cc_start: 0.9294 (m-10) cc_final: 0.8883 (m-80) REVERT: A 511 TYR cc_start: 0.8781 (t80) cc_final: 0.7917 (t80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.0804 time to fit residues: 18.1397 Evaluate side-chains 172 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.4980 chunk 215 optimal weight: 0.0070 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.4980 chunk 470 optimal weight: 10.0000 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108343 restraints weight = 8978.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111590 restraints weight = 5829.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114069 restraints weight = 4182.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115847 restraints weight = 3212.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117220 restraints weight = 2600.543| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 1.614 40068 Z= 1.224 Angle : 1.008 26.090 54432 Z= 0.513 Chirality : 0.048 0.159 6264 Planarity : 0.007 0.102 6840 Dihedral : 6.221 21.053 5412 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.27 % Allowed : 6.85 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.11), residues: 4788 helix: -1.97 (0.09), residues: 2544 sheet: -2.30 (0.25), residues: 384 loop : -2.69 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 91 TYR 0.024 0.003 TYR C 227 PHE 0.018 0.003 PHE A 262 TRP 0.008 0.001 TRP C 489 HIS 0.009 0.001 HIS F 63 Details of bonding type rmsd covalent geometry : bond 0.03565 (40068) covalent geometry : angle 1.00803 (54432) hydrogen bonds : bond 0.07876 ( 1822) hydrogen bonds : angle 6.70101 ( 5286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8096 (ttt-90) REVERT: A 31 PHE cc_start: 0.8586 (m-80) cc_final: 0.8179 (m-80) REVERT: A 35 GLN cc_start: 0.9429 (mm-40) cc_final: 0.8849 (tp40) REVERT: A 49 ASN cc_start: 0.8317 (t0) cc_final: 0.8011 (m110) REVERT: A 50 LEU cc_start: 0.9490 (pt) cc_final: 0.9135 (pt) REVERT: A 61 PHE cc_start: 0.9196 (t80) cc_final: 0.8991 (t80) REVERT: A 65 PHE cc_start: 0.9047 (t80) cc_final: 0.8777 (t80) REVERT: A 138 TYR cc_start: 0.8425 (t80) cc_final: 0.8133 (t80) REVERT: A 141 TYR cc_start: 0.9708 (t80) cc_final: 0.9417 (t80) REVERT: A 151 VAL cc_start: 0.9252 (m) cc_final: 0.8977 (m) REVERT: A 234 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8492 (ttp80) REVERT: A 235 LEU cc_start: 0.8228 (tp) cc_final: 0.7968 (tp) REVERT: A 255 GLN cc_start: 0.9126 (tt0) cc_final: 0.8865 (tt0) REVERT: A 259 GLN cc_start: 0.9223 (pm20) cc_final: 0.9020 (pm20) REVERT: A 263 MET cc_start: 0.9014 (tmm) cc_final: 0.8685 (tmm) REVERT: A 266 ARG cc_start: 0.8277 (mmt-90) cc_final: 0.7960 (mtt90) REVERT: A 448 PHE cc_start: 0.8663 (m-80) cc_final: 0.8366 (m-80) REVERT: A 455 LEU cc_start: 0.8877 (tp) cc_final: 0.8674 (tp) REVERT: A 471 VAL cc_start: 0.8825 (p) cc_final: 0.8563 (p) REVERT: A 483 LYS cc_start: 0.9480 (tppp) cc_final: 0.8871 (tmtt) REVERT: A 489 TRP cc_start: 0.9441 (m100) cc_final: 0.9114 (m100) REVERT: A 492 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 493 LEU cc_start: 0.9343 (mt) cc_final: 0.8678 (mt) REVERT: A 494 PHE cc_start: 0.9344 (m-10) cc_final: 0.9053 (m-80) REVERT: A 511 TYR cc_start: 0.8805 (t80) cc_final: 0.7964 (t80) REVERT: A 514 TYR cc_start: 0.8103 (m-80) cc_final: 0.7884 (m-80) REVERT: A 545 THR cc_start: 0.8636 (t) cc_final: 0.8155 (t) REVERT: A 546 LEU cc_start: 0.8270 (tp) cc_final: 0.8047 (tp) REVERT: A 564 TYR cc_start: 0.9124 (m-80) cc_final: 0.8581 (m-80) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.0861 time to fit residues: 18.8587 Evaluate side-chains 155 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 319 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 422 optimal weight: 0.0070 chunk 343 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110375 restraints weight = 8922.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113441 restraints weight = 6016.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115709 restraints weight = 4417.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117464 restraints weight = 3454.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118453 restraints weight = 2826.933| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 1.617 40068 Z= 1.221 Angle : 0.971 26.175 54432 Z= 0.499 Chirality : 0.049 0.214 6264 Planarity : 0.005 0.035 6840 Dihedral : 5.804 22.220 5412 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 26.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.11), residues: 4788 helix: -1.58 (0.09), residues: 2520 sheet: -1.31 (0.30), residues: 264 loop : -2.38 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 570 TYR 0.023 0.002 TYR G 265 PHE 0.052 0.003 PHE K 470 TRP 0.023 0.002 TRP J 81 HIS 0.005 0.001 HIS F 63 Details of bonding type rmsd covalent geometry : bond 0.03559 (40068) covalent geometry : angle 0.97081 (54432) hydrogen bonds : bond 0.07398 ( 1822) hydrogen bonds : angle 6.44287 ( 5286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 29 ARG cc_start: 0.8965 (ttm-80) cc_final: 0.8645 (ttt180) REVERT: K 31 PHE cc_start: 0.8487 (m-80) cc_final: 0.8066 (m-80) REVERT: K 35 GLN cc_start: 0.9383 (mm-40) cc_final: 0.8830 (tp40) REVERT: K 49 ASN cc_start: 0.8106 (t0) cc_final: 0.7879 (m110) REVERT: K 67 ARG cc_start: 0.9056 (tpp-160) cc_final: 0.8829 (tpp-160) REVERT: K 71 HIS cc_start: 0.7203 (m170) cc_final: 0.6503 (t-170) REVERT: K 82 ASN cc_start: 0.9119 (m-40) cc_final: 0.8919 (m-40) REVERT: K 92 TRP cc_start: 0.6330 (t60) cc_final: 0.6031 (t-100) REVERT: K 138 TYR cc_start: 0.8446 (t80) cc_final: 0.8158 (t80) REVERT: K 140 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8718 (mmm-85) REVERT: K 151 VAL cc_start: 0.8930 (m) cc_final: 0.8713 (m) REVERT: K 155 LYS cc_start: 0.7580 (tptt) cc_final: 0.7298 (tptp) REVERT: K 199 ILE cc_start: 0.9413 (tp) cc_final: 0.9124 (tp) REVERT: K 203 ASN cc_start: 0.8682 (m-40) cc_final: 0.8083 (m-40) REVERT: K 223 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8539 (mt-10) REVERT: K 235 LEU cc_start: 0.8475 (tp) cc_final: 0.7664 (mt) REVERT: K 264 CYS cc_start: 0.9088 (t) cc_final: 0.8754 (t) REVERT: K 435 ILE cc_start: 0.8440 (mt) cc_final: 0.8237 (mm) REVERT: K 483 LYS cc_start: 0.9359 (tppp) cc_final: 0.8917 (tmtt) REVERT: K 489 TRP cc_start: 0.9552 (m100) cc_final: 0.9307 (t-100) REVERT: K 493 LEU cc_start: 0.9304 (mt) cc_final: 0.8696 (mt) REVERT: K 509 ARG cc_start: 0.8415 (mmt90) cc_final: 0.8188 (mtm110) REVERT: K 511 TYR cc_start: 0.8770 (t80) cc_final: 0.8057 (t80) REVERT: K 513 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.6799 (ttp-170) REVERT: K 545 THR cc_start: 0.8893 (t) cc_final: 0.7863 (t) REVERT: K 546 LEU cc_start: 0.8268 (tp) cc_final: 0.8006 (tp) REVERT: K 570 ARG cc_start: 0.9071 (tpm170) cc_final: 0.8503 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0721 time to fit residues: 15.7375 Evaluate side-chains 156 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 462 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 365 optimal weight: 0.0020 chunk 269 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 436 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 465 optimal weight: 8.9990 overall best weight: 4.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106574 restraints weight = 8820.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109561 restraints weight = 5865.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111880 restraints weight = 4277.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113546 restraints weight = 3317.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114911 restraints weight = 2697.601| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40068 Z= 0.190 Angle : 0.783 7.986 54432 Z= 0.424 Chirality : 0.049 0.201 6264 Planarity : 0.005 0.054 6840 Dihedral : 5.544 21.971 5412 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.27 % Allowed : 4.93 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.11), residues: 4788 helix: -1.26 (0.09), residues: 2544 sheet: -1.48 (0.27), residues: 264 loop : -2.48 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 128 TYR 0.019 0.002 TYR J 265 PHE 0.023 0.003 PHE G 470 TRP 0.012 0.002 TRP J 81 HIS 0.008 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00386 (40068) covalent geometry : angle 0.78336 (54432) hydrogen bonds : bond 0.06876 ( 1822) hydrogen bonds : angle 6.21537 ( 5286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8754 (tp40) REVERT: F 67 ARG cc_start: 0.8993 (tpp-160) cc_final: 0.8534 (tpp-160) REVERT: F 75 ASP cc_start: 0.8891 (t70) cc_final: 0.8667 (t0) REVERT: F 81 TRP cc_start: 0.7679 (t60) cc_final: 0.7128 (t60) REVERT: F 140 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8750 (mtm110) REVERT: F 151 VAL cc_start: 0.8988 (m) cc_final: 0.8725 (m) REVERT: F 183 THR cc_start: 0.9205 (p) cc_final: 0.8998 (p) REVERT: F 235 LEU cc_start: 0.8506 (tp) cc_final: 0.8087 (mt) REVERT: F 261 ILE cc_start: 0.9763 (mt) cc_final: 0.9558 (mt) REVERT: F 263 MET cc_start: 0.9029 (tmm) cc_final: 0.8636 (tmm) REVERT: F 264 CYS cc_start: 0.9115 (t) cc_final: 0.8671 (t) REVERT: F 455 LEU cc_start: 0.8785 (tp) cc_final: 0.8572 (tp) REVERT: F 458 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7423 (tmt170) REVERT: F 481 MET cc_start: 0.9083 (tpp) cc_final: 0.8373 (tpp) REVERT: F 483 LYS cc_start: 0.9438 (tppp) cc_final: 0.8915 (tmtt) REVERT: F 489 TRP cc_start: 0.9536 (m100) cc_final: 0.9054 (t-100) REVERT: F 493 LEU cc_start: 0.9346 (mt) cc_final: 0.8923 (mt) REVERT: F 509 ARG cc_start: 0.8239 (mmt90) cc_final: 0.8034 (mtp-110) REVERT: F 511 TYR cc_start: 0.8670 (t80) cc_final: 0.7987 (t80) REVERT: F 513 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.6767 (ttp-170) REVERT: F 545 THR cc_start: 0.8701 (t) cc_final: 0.7740 (t) REVERT: F 546 LEU cc_start: 0.8329 (tp) cc_final: 0.7952 (tp) REVERT: F 551 ILE cc_start: 0.9101 (pt) cc_final: 0.8859 (pt) REVERT: F 570 ARG cc_start: 0.9113 (tpm170) cc_final: 0.8626 (ptt-90) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0694 time to fit residues: 15.0355 Evaluate side-chains 155 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 182 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 465 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 299 optimal weight: 0.0470 chunk 72 optimal weight: 2.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110684 restraints weight = 8476.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113577 restraints weight = 5760.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115893 restraints weight = 4293.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117556 restraints weight = 3356.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118741 restraints weight = 2754.681| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40068 Z= 0.171 Angle : 0.802 7.787 54432 Z= 0.426 Chirality : 0.049 0.185 6264 Planarity : 0.005 0.046 6840 Dihedral : 5.629 22.657 5412 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.11), residues: 4788 helix: -1.25 (0.09), residues: 2580 sheet: -1.03 (0.27), residues: 264 loop : -2.83 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 182 TYR 0.022 0.002 TYR C 74 PHE 0.017 0.002 PHE D 31 TRP 0.014 0.002 TRP G 92 HIS 0.019 0.003 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00368 (40068) covalent geometry : angle 0.80218 (54432) hydrogen bonds : bond 0.06720 ( 1822) hydrogen bonds : angle 6.07440 ( 5286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 PHE cc_start: 0.8582 (m-80) cc_final: 0.8036 (m-80) REVERT: H 35 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8770 (tp40) REVERT: H 50 LEU cc_start: 0.9325 (pt) cc_final: 0.8880 (pt) REVERT: H 82 ASN cc_start: 0.9127 (m110) cc_final: 0.8887 (m-40) REVERT: H 92 TRP cc_start: 0.5950 (t60) cc_final: 0.5514 (t-100) REVERT: H 140 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8712 (mtm110) REVERT: H 165 LYS cc_start: 0.5451 (tmmt) cc_final: 0.4824 (tmmt) REVERT: H 199 ILE cc_start: 0.9319 (tp) cc_final: 0.9092 (tp) REVERT: H 203 ASN cc_start: 0.8728 (m-40) cc_final: 0.8352 (m-40) REVERT: H 220 ARG cc_start: 0.7739 (ptt-90) cc_final: 0.7031 (ptt90) REVERT: H 223 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8155 (mt-10) REVERT: H 225 VAL cc_start: 0.7685 (t) cc_final: 0.7460 (p) REVERT: H 235 LEU cc_start: 0.8701 (tp) cc_final: 0.8444 (mt) REVERT: H 263 MET cc_start: 0.8985 (tmm) cc_final: 0.8661 (tmm) REVERT: H 264 CYS cc_start: 0.9208 (t) cc_final: 0.8704 (t) REVERT: H 272 LYS cc_start: 0.8480 (tttt) cc_final: 0.8233 (tmmt) REVERT: H 278 ASN cc_start: 0.9337 (p0) cc_final: 0.9129 (p0) REVERT: H 473 GLN cc_start: 0.9108 (pm20) cc_final: 0.8755 (pp30) REVERT: H 481 MET cc_start: 0.9134 (tpp) cc_final: 0.8426 (tpp) REVERT: H 483 LYS cc_start: 0.9431 (tppp) cc_final: 0.8941 (tmtt) REVERT: H 489 TRP cc_start: 0.9548 (m100) cc_final: 0.9204 (t-100) REVERT: H 496 THR cc_start: 0.8675 (t) cc_final: 0.8222 (t) REVERT: H 509 ARG cc_start: 0.8252 (mmt90) cc_final: 0.8047 (mtp-110) REVERT: H 511 TYR cc_start: 0.8680 (t80) cc_final: 0.7964 (t80) REVERT: H 526 PHE cc_start: 0.9291 (t80) cc_final: 0.8989 (t80) REVERT: H 545 THR cc_start: 0.8802 (t) cc_final: 0.8202 (t) REVERT: H 546 LEU cc_start: 0.8321 (tp) cc_final: 0.8090 (tp) REVERT: H 554 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9115 (tm-30) REVERT: H 570 ARG cc_start: 0.9148 (tpm170) cc_final: 0.8564 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0674 time to fit residues: 15.3965 Evaluate side-chains 156 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 368 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 437 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108281 restraints weight = 8453.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111136 restraints weight = 5559.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113334 restraints weight = 4037.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114963 restraints weight = 3118.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116088 restraints weight = 2517.743| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 40068 Z= 0.177 Angle : 0.789 7.977 54432 Z= 0.425 Chirality : 0.050 0.217 6264 Planarity : 0.005 0.041 6840 Dihedral : 5.578 21.816 5412 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.11), residues: 4788 helix: -1.14 (0.09), residues: 2580 sheet: -1.47 (0.27), residues: 384 loop : -2.73 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 509 TYR 0.021 0.002 TYR B 47 PHE 0.013 0.002 PHE G 448 TRP 0.016 0.002 TRP J 489 HIS 0.014 0.002 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00384 (40068) covalent geometry : angle 0.78920 (54432) hydrogen bonds : bond 0.06674 ( 1822) hydrogen bonds : angle 6.19626 ( 5286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 29 ARG cc_start: 0.8793 (mtp180) cc_final: 0.7794 (ttt-90) REVERT: K 31 PHE cc_start: 0.8735 (m-80) cc_final: 0.8143 (m-80) REVERT: K 35 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8849 (tp40) REVERT: K 49 ASN cc_start: 0.7971 (m110) cc_final: 0.7599 (m110) REVERT: K 71 HIS cc_start: 0.7285 (m170) cc_final: 0.6763 (t-170) REVERT: K 82 ASN cc_start: 0.8902 (m110) cc_final: 0.8580 (m-40) REVERT: K 140 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8559 (mtm110) REVERT: K 223 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8487 (mt-10) REVERT: K 235 LEU cc_start: 0.8631 (tp) cc_final: 0.8202 (mt) REVERT: K 255 GLN cc_start: 0.9124 (tt0) cc_final: 0.8766 (pt0) REVERT: K 262 PHE cc_start: 0.8421 (m-80) cc_final: 0.7894 (m-80) REVERT: K 264 CYS cc_start: 0.9261 (t) cc_final: 0.8918 (t) REVERT: K 270 HIS cc_start: 0.8809 (t-90) cc_final: 0.8589 (t-90) REVERT: K 483 LYS cc_start: 0.9381 (tppp) cc_final: 0.8977 (tmtt) REVERT: K 492 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8125 (tm-30) REVERT: K 493 LEU cc_start: 0.9516 (mt) cc_final: 0.9081 (mt) REVERT: K 511 TYR cc_start: 0.8597 (t80) cc_final: 0.7919 (t80) REVERT: K 514 TYR cc_start: 0.8060 (m-80) cc_final: 0.7724 (m-80) REVERT: K 518 THR cc_start: 0.8945 (t) cc_final: 0.8644 (t) REVERT: K 526 PHE cc_start: 0.9363 (t80) cc_final: 0.8938 (t80) REVERT: K 545 THR cc_start: 0.9010 (t) cc_final: 0.8572 (t) REVERT: K 546 LEU cc_start: 0.8304 (tp) cc_final: 0.8056 (tp) REVERT: K 570 ARG cc_start: 0.9004 (tpm170) cc_final: 0.8627 (ptt90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0615 time to fit residues: 13.7816 Evaluate side-chains 156 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 279 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 329 optimal weight: 0.2980 chunk 381 optimal weight: 0.0070 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108311 restraints weight = 8740.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111230 restraints weight = 5808.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113388 restraints weight = 4279.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115097 restraints weight = 3368.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116426 restraints weight = 2765.575| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40068 Z= 0.169 Angle : 0.827 8.520 54432 Z= 0.437 Chirality : 0.050 0.207 6264 Planarity : 0.005 0.044 6840 Dihedral : 5.507 24.025 5412 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.11), residues: 4788 helix: -1.22 (0.09), residues: 2604 sheet: -0.80 (0.27), residues: 264 loop : -2.78 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 509 TYR 0.021 0.002 TYR F 265 PHE 0.025 0.002 PHE G 497 TRP 0.035 0.002 TRP B 489 HIS 0.011 0.002 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00364 (40068) covalent geometry : angle 0.82671 (54432) hydrogen bonds : bond 0.06459 ( 1822) hydrogen bonds : angle 6.23462 ( 5286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 29 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8505 (ttt180) REVERT: K 35 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8739 (tp40) REVERT: K 49 ASN cc_start: 0.8004 (m110) cc_final: 0.7607 (m110) REVERT: K 67 ARG cc_start: 0.8583 (tpm170) cc_final: 0.8028 (tpp-160) REVERT: K 114 MET cc_start: 0.8710 (mmp) cc_final: 0.8460 (mmm) REVERT: K 117 THR cc_start: 0.8578 (p) cc_final: 0.8373 (p) REVERT: K 140 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8543 (mtm110) REVERT: K 197 GLU cc_start: 0.9525 (mp0) cc_final: 0.9308 (mp0) REVERT: K 209 GLN cc_start: 0.8273 (pp30) cc_final: 0.7967 (pp30) REVERT: K 223 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8432 (mt-10) REVERT: K 234 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8499 (ttp80) REVERT: K 235 LEU cc_start: 0.8583 (tp) cc_final: 0.8342 (tp) REVERT: K 255 GLN cc_start: 0.9224 (tt0) cc_final: 0.8879 (pt0) REVERT: K 270 HIS cc_start: 0.8748 (t-90) cc_final: 0.8500 (t-90) REVERT: K 483 LYS cc_start: 0.9252 (tppp) cc_final: 0.8997 (tmtt) REVERT: K 492 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8201 (tm-30) REVERT: K 493 LEU cc_start: 0.9497 (mt) cc_final: 0.9066 (mt) REVERT: K 494 PHE cc_start: 0.7440 (m-80) cc_final: 0.6738 (m-80) REVERT: K 504 ASP cc_start: 0.7805 (t0) cc_final: 0.7590 (t70) REVERT: K 511 TYR cc_start: 0.8537 (t80) cc_final: 0.7944 (t80) REVERT: K 513 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.6732 (ttp-170) REVERT: K 514 TYR cc_start: 0.7898 (m-80) cc_final: 0.7683 (m-80) REVERT: K 518 THR cc_start: 0.8946 (t) cc_final: 0.8624 (t) REVERT: K 526 PHE cc_start: 0.9367 (t80) cc_final: 0.8990 (t80) REVERT: K 545 THR cc_start: 0.9012 (t) cc_final: 0.7908 (t) REVERT: K 546 LEU cc_start: 0.8263 (tp) cc_final: 0.8049 (tp) REVERT: K 570 ARG cc_start: 0.9036 (tpm170) cc_final: 0.8638 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0701 time to fit residues: 15.4248 Evaluate side-chains 155 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 134 optimal weight: 0.3980 chunk 260 optimal weight: 0.0670 chunk 170 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 453 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 451 optimal weight: 20.0000 overall best weight: 2.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 131 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109314 restraints weight = 8874.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112369 restraints weight = 5866.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.114623 restraints weight = 4287.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116236 restraints weight = 3343.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117550 restraints weight = 2749.124| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.8087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40068 Z= 0.174 Angle : 0.822 8.032 54432 Z= 0.432 Chirality : 0.052 0.197 6264 Planarity : 0.006 0.048 6840 Dihedral : 5.605 24.151 5412 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.11), residues: 4788 helix: -1.06 (0.09), residues: 2628 sheet: -0.64 (0.26), residues: 264 loop : -2.78 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 509 TYR 0.022 0.002 TYR F 47 PHE 0.018 0.002 PHE H 31 TRP 0.034 0.002 TRP L 489 HIS 0.011 0.002 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00380 (40068) covalent geometry : angle 0.82162 (54432) hydrogen bonds : bond 0.06210 ( 1822) hydrogen bonds : angle 6.16224 ( 5286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 ARG cc_start: 0.8753 (mtp180) cc_final: 0.7979 (ttt180) REVERT: G 31 PHE cc_start: 0.8873 (m-80) cc_final: 0.8135 (m-80) REVERT: G 35 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8778 (tp40) REVERT: G 67 ARG cc_start: 0.8657 (tpm170) cc_final: 0.8081 (tpp-160) REVERT: G 75 ASP cc_start: 0.9086 (t70) cc_final: 0.8514 (t0) REVERT: G 80 ASP cc_start: 0.8945 (t0) cc_final: 0.8644 (t0) REVERT: G 131 HIS cc_start: 0.8230 (p90) cc_final: 0.7864 (p90) REVERT: G 165 LYS cc_start: 0.5780 (tmmt) cc_final: 0.5426 (tmmt) REVERT: G 255 GLN cc_start: 0.9286 (tt0) cc_final: 0.8907 (pt0) REVERT: G 262 PHE cc_start: 0.8658 (m-80) cc_final: 0.8160 (m-80) REVERT: G 264 CYS cc_start: 0.9146 (t) cc_final: 0.8842 (t) REVERT: G 458 ARG cc_start: 0.6890 (tmt170) cc_final: 0.6309 (tmt170) REVERT: G 479 ARG cc_start: 0.8615 (tmt170) cc_final: 0.8205 (ttp80) REVERT: G 483 LYS cc_start: 0.9313 (tppp) cc_final: 0.8807 (tmtt) REVERT: G 492 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 493 LEU cc_start: 0.9501 (mt) cc_final: 0.9133 (mt) REVERT: G 494 PHE cc_start: 0.7712 (m-80) cc_final: 0.7089 (m-80) REVERT: G 496 THR cc_start: 0.8746 (t) cc_final: 0.8544 (t) REVERT: G 511 TYR cc_start: 0.8435 (t80) cc_final: 0.7880 (t80) REVERT: G 513 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.6598 (ttp-170) REVERT: G 518 THR cc_start: 0.8991 (t) cc_final: 0.8699 (t) REVERT: G 545 THR cc_start: 0.8900 (t) cc_final: 0.7910 (t) REVERT: G 546 LEU cc_start: 0.8095 (tp) cc_final: 0.7880 (tp) REVERT: G 570 ARG cc_start: 0.9098 (tpm170) cc_final: 0.8682 (ptt180) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.0733 time to fit residues: 16.3650 Evaluate side-chains 165 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 448 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 chunk 413 optimal weight: 0.0030 chunk 388 optimal weight: 0.0770 chunk 310 optimal weight: 10.0000 chunk 414 optimal weight: 0.4980 chunk 287 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112556 restraints weight = 8595.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115536 restraints weight = 5584.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117986 restraints weight = 4078.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119772 restraints weight = 3121.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121118 restraints weight = 2515.858| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.8347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40068 Z= 0.171 Angle : 0.866 10.245 54432 Z= 0.449 Chirality : 0.051 0.236 6264 Planarity : 0.006 0.053 6840 Dihedral : 5.497 25.698 5412 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.11), residues: 4788 helix: -1.35 (0.09), residues: 2604 sheet: -0.70 (0.26), residues: 264 loop : -2.88 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.025 0.002 TYR C 265 PHE 0.018 0.002 PHE C 497 TRP 0.065 0.003 TRP G 489 HIS 0.010 0.001 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00373 (40068) covalent geometry : angle 0.86630 (54432) hydrogen bonds : bond 0.06363 ( 1822) hydrogen bonds : angle 6.19608 ( 5286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 ARG cc_start: 0.8928 (mtp180) cc_final: 0.8087 (ttt180) REVERT: F 31 PHE cc_start: 0.8830 (m-80) cc_final: 0.8485 (m-80) REVERT: F 35 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8441 (tp40) REVERT: F 50 LEU cc_start: 0.9439 (pt) cc_final: 0.8889 (pt) REVERT: F 67 ARG cc_start: 0.8738 (tpm170) cc_final: 0.8368 (tpp-160) REVERT: F 75 ASP cc_start: 0.9261 (t70) cc_final: 0.9001 (t0) REVERT: F 80 ASP cc_start: 0.8867 (t0) cc_final: 0.8468 (t0) REVERT: F 81 TRP cc_start: 0.7755 (t60) cc_final: 0.7138 (t60) REVERT: F 92 TRP cc_start: 0.8115 (t-100) cc_final: 0.7641 (t-100) REVERT: F 128 ARG cc_start: 0.8416 (tpm170) cc_final: 0.8115 (tpm170) REVERT: F 165 LYS cc_start: 0.5674 (tmmt) cc_final: 0.5011 (tmmt) REVERT: F 197 GLU cc_start: 0.9485 (mp0) cc_final: 0.9218 (mp0) REVERT: F 209 GLN cc_start: 0.9013 (pp30) cc_final: 0.8746 (pp30) REVERT: F 223 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8117 (mt-10) REVERT: F 234 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8530 (ttp80) REVERT: F 235 LEU cc_start: 0.8544 (tp) cc_final: 0.8306 (tp) REVERT: F 255 GLN cc_start: 0.9300 (tt0) cc_final: 0.8862 (pt0) REVERT: F 270 HIS cc_start: 0.8816 (t-90) cc_final: 0.8459 (t-90) REVERT: F 480 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8880 (mm-30) REVERT: F 481 MET cc_start: 0.9295 (tpp) cc_final: 0.8846 (tpp) REVERT: F 483 LYS cc_start: 0.9375 (tppp) cc_final: 0.8831 (tmtt) REVERT: F 492 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8362 (tm-30) REVERT: F 493 LEU cc_start: 0.9421 (mt) cc_final: 0.8979 (mt) REVERT: F 494 PHE cc_start: 0.7952 (m-80) cc_final: 0.7337 (m-80) REVERT: F 511 TYR cc_start: 0.8378 (t80) cc_final: 0.7877 (t80) REVERT: F 526 PHE cc_start: 0.9101 (t80) cc_final: 0.8641 (t80) REVERT: F 545 THR cc_start: 0.8832 (t) cc_final: 0.8373 (t) REVERT: F 570 ARG cc_start: 0.8930 (tpm170) cc_final: 0.8550 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0673 time to fit residues: 15.4664 Evaluate side-chains 164 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 248 optimal weight: 5.9990 chunk 375 optimal weight: 0.0670 chunk 420 optimal weight: 0.0070 chunk 424 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 403 optimal weight: 8.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113354 restraints weight = 8660.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116542 restraints weight = 5668.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118885 restraints weight = 4090.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120609 restraints weight = 3155.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121962 restraints weight = 2553.087| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.8559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40068 Z= 0.162 Angle : 0.828 8.639 54432 Z= 0.428 Chirality : 0.051 0.239 6264 Planarity : 0.006 0.057 6840 Dihedral : 5.328 23.973 5412 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.11), residues: 4788 helix: -1.34 (0.09), residues: 2580 sheet: -0.64 (0.25), residues: 264 loop : -2.88 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 509 TYR 0.021 0.002 TYR L 40 PHE 0.020 0.002 PHE J 497 TRP 0.047 0.003 TRP G 489 HIS 0.010 0.001 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00347 (40068) covalent geometry : angle 0.82807 (54432) hydrogen bonds : bond 0.06216 ( 1822) hydrogen bonds : angle 5.99156 ( 5286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 ARG cc_start: 0.8973 (mtp180) cc_final: 0.8183 (ttt-90) REVERT: F 31 PHE cc_start: 0.8850 (m-80) cc_final: 0.8529 (m-80) REVERT: F 32 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7542 (tm-30) REVERT: F 35 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8408 (tp40) REVERT: F 50 LEU cc_start: 0.9449 (pt) cc_final: 0.8913 (pt) REVERT: F 67 ARG cc_start: 0.8705 (tpm170) cc_final: 0.8359 (tpp-160) REVERT: F 75 ASP cc_start: 0.9159 (t70) cc_final: 0.8837 (t0) REVERT: F 79 HIS cc_start: 0.8885 (p-80) cc_final: 0.8663 (p90) REVERT: F 80 ASP cc_start: 0.8869 (t0) cc_final: 0.8431 (t0) REVERT: F 81 TRP cc_start: 0.7701 (t60) cc_final: 0.7305 (t60) REVERT: F 92 TRP cc_start: 0.8034 (t-100) cc_final: 0.7606 (t-100) REVERT: F 107 PHE cc_start: 0.9151 (t80) cc_final: 0.8731 (t80) REVERT: F 223 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7972 (mt-10) REVERT: F 234 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8559 (ttp80) REVERT: F 255 GLN cc_start: 0.9303 (tt0) cc_final: 0.8920 (pt0) REVERT: F 270 HIS cc_start: 0.8919 (t-90) cc_final: 0.8444 (t-90) REVERT: F 272 LYS cc_start: 0.7740 (tttt) cc_final: 0.7486 (tmmt) REVERT: F 480 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8861 (mm-30) REVERT: F 481 MET cc_start: 0.9358 (tpp) cc_final: 0.8951 (tpp) REVERT: F 483 LYS cc_start: 0.9413 (tppp) cc_final: 0.8791 (tmtt) REVERT: F 492 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8375 (tm-30) REVERT: F 493 LEU cc_start: 0.9334 (mt) cc_final: 0.8924 (mt) REVERT: F 494 PHE cc_start: 0.7938 (m-80) cc_final: 0.7004 (m-80) REVERT: F 511 TYR cc_start: 0.8299 (t80) cc_final: 0.7814 (t80) REVERT: F 526 PHE cc_start: 0.8965 (t80) cc_final: 0.8589 (t80) REVERT: F 545 THR cc_start: 0.8827 (t) cc_final: 0.8281 (t) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0658 time to fit residues: 14.6793 Evaluate side-chains 155 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 80 optimal weight: 10.0000 chunk 428 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 404 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 395 optimal weight: 0.0070 chunk 42 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 44 GLN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111801 restraints weight = 8818.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114965 restraints weight = 5783.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117317 restraints weight = 4173.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119116 restraints weight = 3236.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120455 restraints weight = 2635.934| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40068 Z= 0.181 Angle : 0.886 11.457 54432 Z= 0.459 Chirality : 0.052 0.251 6264 Planarity : 0.006 0.059 6840 Dihedral : 5.296 25.317 5412 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.11), residues: 4788 helix: -1.49 (0.09), residues: 2580 sheet: -0.83 (0.23), residues: 264 loop : -2.94 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 509 TYR 0.024 0.002 TYR I 40 PHE 0.020 0.003 PHE I 102 TRP 0.040 0.003 TRP L 489 HIS 0.009 0.001 HIS I 63 Details of bonding type rmsd covalent geometry : bond 0.00397 (40068) covalent geometry : angle 0.88601 (54432) hydrogen bonds : bond 0.06318 ( 1822) hydrogen bonds : angle 5.97201 ( 5286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.71 seconds wall clock time: 39 minutes 41.85 seconds (2381.85 seconds total)