Starting phenix.real_space_refine on Tue Sep 15 10:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bqt_30155/09_2026/7bqt_30155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bqt_30155/09_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_30155/09_2026/7bqt_30155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bqt_30155/09_2026/7bqt_30155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bqt_30155/09_2026/7bqt_30155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bqt_30155/09_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.97, 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: 3.36 Conformation dependent library (CDL) restraints added in 1.5 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: 1.39 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: 7.27 Time building geometry restraints manager: 4.42 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: 0.02 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 33.360 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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/Z covalent geometry : bond 0.00579 / 0.28 (40068) covalent geometry : angle 1.07026 / 0.58 (54432) hydrogen bonds : bond 0.20188 / 13.22 ( 1822) hydrogen bonds : angle 8.20254 / 5.76 ( 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 : 0.126 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: 0.0741 time to fit residues: 16.9617 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 : 0.126 ------------------------------------------------------------------------------- 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... ** 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 = 0.3721 r_free = 0.3721 target = 0.129418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107816 restraints weight = 8907.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110892 restraints weight = 5899.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113251 restraints weight = 4296.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115002 restraints weight = 3319.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116418 restraints weight = 2696.265| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5599 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 26.082 54432 Z= 0.513 Chirality : 0.048 0.159 6264 Planarity : 0.007 0.102 6840 Dihedral : 6.220 21.050 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 : 0.00 % Allowed : 6.85 % Favored : 93.15 % 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 A 91 TYR 0.024 0.003 TYR I 227 PHE 0.018 0.003 PHE A 262 TRP 0.008 0.001 TRP J 489 HIS 0.009 0.001 HIS F 63 Details of bonding type rmsd/Z covalent geometry : bond 0.03564 / 1.22 (40068) covalent geometry : angle 1.00783 / 0.51 (54432) hydrogen bonds : bond 0.07874 / 5.02 ( 1822) hydrogen bonds : angle 6.70073 / 4.67 ( 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 193 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 29 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8329 (ttt-90) REVERT: L 31 PHE cc_start: 0.8236 (m-80) cc_final: 0.7885 (m-80) REVERT: L 35 GLN cc_start: 0.9452 (mm-40) cc_final: 0.8716 (tp40) REVERT: L 49 ASN cc_start: 0.8275 (t0) cc_final: 0.8061 (m110) REVERT: L 67 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8554 (tpp-160) REVERT: L 81 TRP cc_start: 0.8078 (t60) cc_final: 0.7394 (t60) REVERT: L 107 PHE cc_start: 0.9063 (t80) cc_final: 0.8684 (t80) REVERT: L 138 TYR cc_start: 0.8321 (t80) cc_final: 0.8038 (t80) REVERT: L 140 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8421 (mtm-85) REVERT: L 141 TYR cc_start: 0.9630 (t80) cc_final: 0.9371 (t80) REVERT: L 151 VAL cc_start: 0.9079 (m) cc_final: 0.8696 (m) REVERT: L 190 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8688 (pp20) REVERT: L 235 LEU cc_start: 0.8512 (tp) cc_final: 0.7261 (mt) REVERT: L 236 HIS cc_start: 0.7825 (m170) cc_final: 0.7269 (m170) REVERT: L 255 GLN cc_start: 0.8997 (tt0) cc_final: 0.8744 (tt0) REVERT: L 270 HIS cc_start: 0.8675 (t-90) cc_final: 0.8330 (t-90) REVERT: L 448 PHE cc_start: 0.8591 (m-80) cc_final: 0.8321 (m-80) REVERT: L 473 GLN cc_start: 0.9131 (pm20) cc_final: 0.8756 (pp30) REVERT: L 483 LYS cc_start: 0.9502 (tppp) cc_final: 0.8960 (tmtt) REVERT: L 489 TRP cc_start: 0.9543 (m100) cc_final: 0.9188 (m100) REVERT: L 494 PHE cc_start: 0.9353 (m-10) cc_final: 0.8912 (m-80) REVERT: L 496 THR cc_start: 0.8801 (t) cc_final: 0.8548 (t) REVERT: L 511 TYR cc_start: 0.8767 (t80) cc_final: 0.8003 (t80) REVERT: L 514 TYR cc_start: 0.7862 (m-80) cc_final: 0.7513 (m-80) REVERT: L 545 THR cc_start: 0.8727 (t) cc_final: 0.8195 (t) REVERT: L 546 LEU cc_start: 0.8423 (tp) cc_final: 0.8181 (tp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0685 time to fit residues: 15.5794 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 : 0.136 ------------------------------------------------------------------------------- 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: 9.9990 chunk 307 optimal weight: 10.0000 chunk 422 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 313 optimal weight: 0.0010 chunk 226 optimal weight: 0.0570 chunk 161 optimal weight: 6.9990 chunk 296 optimal weight: 0.0970 chunk 167 optimal weight: 0.0040 chunk 220 optimal weight: 8.9990 overall best weight: 1.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 59 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 = 0.3734 r_free = 0.3734 target = 0.129351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109029 restraints weight = 8834.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112122 restraints weight = 5720.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114433 restraints weight = 4106.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116128 restraints weight = 3148.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117537 restraints weight = 2539.101| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 1.598 40068 Z= 1.214 Angle : 0.958 25.796 54432 Z= 0.490 Chirality : 0.047 0.205 6264 Planarity : 0.006 0.053 6840 Dihedral : 5.789 21.503 5412 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -2.90 (0.11), residues: 4788 helix: -1.47 (0.09), residues: 2532 sheet: -1.25 (0.30), residues: 264 loop : -2.52 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 232 TYR 0.018 0.002 TYR B 224 PHE 0.057 0.003 PHE B 470 TRP 0.011 0.001 TRP C 489 HIS 0.010 0.002 HIS F 131 Details of bonding type rmsd/Z covalent geometry : bond 0.03542 / 1.21 (40068) covalent geometry : angle 0.95773 / 0.49 (54432) hydrogen bonds : bond 0.07415 / 4.73 ( 1822) hydrogen bonds : angle 6.35542 / 4.45 ( 5286) *********************** REFINEMENT MACRO_CYCLE 3 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 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: symmetry clash REVERT: K 31 PHE cc_start: 0.8489 (m-80) cc_final: 0.8067 (m-80) REVERT: K 35 GLN cc_start: 0.9376 (mm-40) cc_final: 0.8921 (tp40) REVERT: K 71 HIS cc_start: 0.7557 (m170) cc_final: 0.6895 (t-170) REVERT: K 75 ASP cc_start: 0.8566 (t0) cc_final: 0.8347 (t0) REVERT: K 82 ASN cc_start: 0.9119 (m-40) cc_final: 0.8908 (m-40) REVERT: K 92 TRP cc_start: 0.6296 (t60) cc_final: 0.5837 (t-100) REVERT: K 138 TYR cc_start: 0.8526 (t80) cc_final: 0.8171 (t80) REVERT: K 140 ARG cc_start: 0.8828 (mtm110) cc_final: 0.8612 (mtm110) REVERT: K 151 VAL cc_start: 0.9028 (m) cc_final: 0.8771 (m) REVERT: K 223 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8534 (mt-10) REVERT: K 235 LEU cc_start: 0.8301 (tp) cc_final: 0.7769 (mt) REVERT: K 263 MET cc_start: 0.9069 (tmm) cc_final: 0.8785 (tmm) REVERT: K 469 SER cc_start: 0.8524 (p) cc_final: 0.8304 (p) REVERT: K 483 LYS cc_start: 0.9285 (tppp) cc_final: 0.8877 (tmtt) REVERT: K 489 TRP cc_start: 0.9523 (m100) cc_final: 0.9093 (t-100) REVERT: K 492 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8590 (tm-30) REVERT: K 493 LEU cc_start: 0.9470 (mt) cc_final: 0.8816 (mt) REVERT: K 511 TYR cc_start: 0.8733 (t80) cc_final: 0.8009 (t80) REVERT: K 513 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.6725 (ttp-170) REVERT: K 545 THR cc_start: 0.8841 (t) cc_final: 0.7763 (t) REVERT: K 546 LEU cc_start: 0.8080 (tp) cc_final: 0.7773 (tp) REVERT: K 570 ARG cc_start: 0.9111 (tpm170) cc_final: 0.8481 (ptm160) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0697 time to fit residues: 15.4841 Evaluate side-chains 157 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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: 20.0000 chunk 365 optimal weight: 0.0870 chunk 269 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 436 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 220 optimal weight: 0.1980 chunk 383 optimal weight: 0.9990 chunk 465 optimal weight: 0.5980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN K 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111269 restraints weight = 8627.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114485 restraints weight = 5769.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117018 restraints weight = 4201.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118906 restraints weight = 3234.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120365 restraints weight = 2604.227| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40068 Z= 0.170 Angle : 0.810 8.967 54432 Z= 0.430 Chirality : 0.050 0.209 6264 Planarity : 0.005 0.041 6840 Dihedral : 5.491 17.027 5412 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: -2.80 (0.11), residues: 4788 helix: -1.25 (0.09), residues: 2544 sheet: -1.36 (0.26), residues: 264 loop : -2.69 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 509 TYR 0.016 0.002 TYR F 224 PHE 0.025 0.003 PHE I 470 TRP 0.014 0.001 TRP I 489 HIS 0.016 0.003 HIS H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (40068) covalent geometry : angle 0.81041 / 0.43 (54432) hydrogen bonds : bond 0.07075 / 4.52 ( 1822) hydrogen bonds : angle 6.23365 / 4.37 ( 5286) *********************** REFINEMENT MACRO_CYCLE 4 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 192 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8571 (tp40) REVERT: H 41 VAL cc_start: 0.9250 (t) cc_final: 0.8929 (t) REVERT: H 75 ASP cc_start: 0.8661 (t0) cc_final: 0.8371 (t0) REVERT: H 156 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8757 (mttt) REVERT: H 199 ILE cc_start: 0.9303 (tp) cc_final: 0.9072 (tp) REVERT: H 203 ASN cc_start: 0.8623 (m-40) cc_final: 0.8142 (m-40) REVERT: H 223 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8225 (mt-10) REVERT: H 235 LEU cc_start: 0.8421 (tp) cc_final: 0.8000 (mt) REVERT: H 236 HIS cc_start: 0.7989 (m170) cc_final: 0.7468 (m170) REVERT: H 263 MET cc_start: 0.8998 (tmm) cc_final: 0.8667 (tmm) REVERT: H 264 CYS cc_start: 0.9144 (t) cc_final: 0.8868 (t) REVERT: H 270 HIS cc_start: 0.8544 (t-90) cc_final: 0.8289 (t-90) REVERT: H 481 MET cc_start: 0.9161 (tpp) cc_final: 0.8486 (tpp) REVERT: H 483 LYS cc_start: 0.9358 (tppp) cc_final: 0.8880 (tmtt) REVERT: H 489 TRP cc_start: 0.9569 (m100) cc_final: 0.9250 (t-100) REVERT: H 493 LEU cc_start: 0.9257 (mt) cc_final: 0.8835 (mt) REVERT: H 509 ARG cc_start: 0.7661 (mmt90) cc_final: 0.7429 (mpt-90) REVERT: H 511 TYR cc_start: 0.8585 (t80) cc_final: 0.7893 (t80) REVERT: H 513 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.6562 (ttp-170) REVERT: H 545 THR cc_start: 0.8703 (t) cc_final: 0.7887 (t) REVERT: H 546 LEU cc_start: 0.8222 (tp) cc_final: 0.7990 (tp) REVERT: H 570 ARG cc_start: 0.9088 (tpm170) cc_final: 0.8660 (ptt90) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.0800 time to fit residues: 17.9270 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 : 0.087 ------------------------------------------------------------------------------- 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: 20.0000 chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 465 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 299 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3659 r_free = 0.3659 target = 0.123973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103477 restraints weight = 8837.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106460 restraints weight = 5800.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108775 restraints weight = 4188.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110353 restraints weight = 3199.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111808 restraints weight = 2584.716| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40068 Z= 0.177 Angle : 0.793 8.326 54432 Z= 0.425 Chirality : 0.049 0.229 6264 Planarity : 0.006 0.037 6840 Dihedral : 5.439 17.261 5412 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 21.35 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: -2.37 (0.11), residues: 4788 helix: -0.86 (0.09), residues: 2556 sheet: -1.59 (0.26), residues: 384 loop : -2.51 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 140 TYR 0.020 0.002 TYR G 47 PHE 0.045 0.003 PHE A 470 TRP 0.020 0.001 TRP A 489 HIS 0.012 0.002 HIS I 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (40068) covalent geometry : angle 0.79256 / 0.43 (54432) hydrogen bonds : bond 0.06568 / 4.20 ( 1822) hydrogen bonds : angle 6.13805 / 4.28 ( 5286) *********************** REFINEMENT MACRO_CYCLE 5 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 177 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: H 31 PHE cc_start: 0.8595 (m-80) cc_final: 0.7949 (m-80) REVERT: H 35 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8700 (tp40) REVERT: H 44 GLN cc_start: 0.8804 (tt0) cc_final: 0.8572 (tt0) REVERT: H 49 ASN cc_start: 0.7779 (m110) cc_final: 0.7512 (m110) REVERT: H 92 TRP cc_start: 0.8328 (t-100) cc_final: 0.7936 (t-100) REVERT: H 190 GLU cc_start: 0.8763 (mp0) cc_final: 0.8553 (mp0) REVERT: H 223 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8167 (mt-10) REVERT: H 235 LEU cc_start: 0.8703 (tp) cc_final: 0.8088 (mt) REVERT: H 236 HIS cc_start: 0.8187 (m170) cc_final: 0.7473 (m170) REVERT: H 263 MET cc_start: 0.9012 (tmm) cc_final: 0.8552 (tmm) REVERT: H 264 CYS cc_start: 0.9183 (t) cc_final: 0.8625 (t) REVERT: H 481 MET cc_start: 0.9073 (tpp) cc_final: 0.8366 (tpp) REVERT: H 483 LYS cc_start: 0.9401 (tppp) cc_final: 0.8937 (tmtt) REVERT: H 489 TRP cc_start: 0.9493 (m100) cc_final: 0.9047 (t-100) REVERT: H 492 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 493 LEU cc_start: 0.9370 (mt) cc_final: 0.8799 (mt) REVERT: H 496 THR cc_start: 0.8744 (t) cc_final: 0.8503 (t) REVERT: H 509 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7669 (mpt-90) REVERT: H 511 TYR cc_start: 0.8635 (t80) cc_final: 0.7880 (t80) REVERT: H 545 THR cc_start: 0.8788 (t) cc_final: 0.8191 (t) REVERT: H 546 LEU cc_start: 0.8236 (tp) cc_final: 0.8004 (tp) REVERT: H 564 TYR cc_start: 0.9021 (m-10) cc_final: 0.8645 (m-80) REVERT: H 570 ARG cc_start: 0.9182 (tpm170) cc_final: 0.8455 (ptm160) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0579 time to fit residues: 12.5953 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 : 0.115 ------------------------------------------------------------------------------- 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: 6.9990 chunk 376 optimal weight: 0.2980 chunk 349 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 288 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 437 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 372 optimal weight: 7.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3755 r_free = 0.3755 target = 0.130159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109618 restraints weight = 8609.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112593 restraints weight = 5536.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114760 restraints weight = 3967.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116225 restraints weight = 3048.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117565 restraints weight = 2490.833| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40068 Z= 0.177 Angle : 0.829 12.137 54432 Z= 0.435 Chirality : 0.052 0.211 6264 Planarity : 0.005 0.040 6840 Dihedral : 5.462 20.062 5412 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -2.29 (0.11), residues: 4788 helix: -0.76 (0.10), residues: 2604 sheet: -0.86 (0.25), residues: 264 loop : -2.66 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 140 TYR 0.026 0.002 TYR G 47 PHE 0.034 0.003 PHE E 470 TRP 0.020 0.001 TRP G 489 HIS 0.010 0.002 HIS I 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (40068) covalent geometry : angle 0.82946 / 0.43 (54432) hydrogen bonds : bond 0.06658 / 4.26 ( 1822) hydrogen bonds : angle 6.16603 / 4.30 ( 5286) *********************** REFINEMENT MACRO_CYCLE 6 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 182 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 31 PHE cc_start: 0.8711 (m-80) cc_final: 0.8130 (m-80) REVERT: K 35 GLN cc_start: 0.9430 (mm-40) cc_final: 0.8844 (tp40) REVERT: K 50 LEU cc_start: 0.9424 (pt) cc_final: 0.9060 (pt) REVERT: K 223 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8440 (mt-10) REVERT: K 235 LEU cc_start: 0.8635 (tp) cc_final: 0.7788 (mt) REVERT: K 239 PHE cc_start: 0.8872 (m-10) cc_final: 0.8669 (m-80) REVERT: K 263 MET cc_start: 0.9159 (tmm) cc_final: 0.8953 (tmm) REVERT: K 264 CYS cc_start: 0.9296 (t) cc_final: 0.8978 (t) REVERT: K 270 HIS cc_start: 0.8855 (t-90) cc_final: 0.8645 (t-90) REVERT: K 483 LYS cc_start: 0.9393 (tppp) cc_final: 0.8990 (tmtt) REVERT: K 492 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8131 (tm-30) REVERT: K 493 LEU cc_start: 0.9507 (mt) cc_final: 0.9083 (mt) REVERT: K 511 TYR cc_start: 0.8480 (t80) cc_final: 0.7861 (t80) REVERT: K 513 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.6749 (ttp-170) REVERT: K 518 THR cc_start: 0.8954 (t) cc_final: 0.8586 (t) REVERT: K 545 THR cc_start: 0.8869 (t) cc_final: 0.7718 (t) REVERT: K 546 LEU cc_start: 0.8257 (tp) cc_final: 0.8019 (tp) REVERT: K 554 GLU cc_start: 0.9528 (tp30) cc_final: 0.9088 (tm-30) REVERT: K 570 ARG cc_start: 0.8931 (tpm170) cc_final: 0.8284 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0696 time to fit residues: 15.2023 Evaluate side-chains 160 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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: 2.9990 chunk 361 optimal weight: 0.0470 chunk 176 optimal weight: 9.9990 chunk 377 optimal weight: 0.4980 chunk 329 optimal weight: 0.0770 chunk 381 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 331 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 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 = 0.3774 r_free = 0.3774 target = 0.132231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111589 restraints weight = 8713.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114692 restraints weight = 5581.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116918 restraints weight = 3986.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118522 restraints weight = 3059.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119949 restraints weight = 2483.821| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40068 Z= 0.168 Angle : 0.855 13.167 54432 Z= 0.439 Chirality : 0.052 0.211 6264 Planarity : 0.006 0.065 6840 Dihedral : 5.443 20.746 5412 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -2.16 (0.11), residues: 4788 helix: -0.71 (0.10), residues: 2628 sheet: -0.55 (0.25), residues: 264 loop : -2.57 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 266 TYR 0.022 0.002 TYR B 265 PHE 0.034 0.002 PHE I 470 TRP 0.015 0.001 TRP C 489 HIS 0.008 0.001 HIS F 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (40068) covalent geometry : angle 0.85511 / 0.44 (54432) hydrogen bonds : bond 0.06397 / 4.12 ( 1822) hydrogen bonds : angle 6.02182 / 4.20 ( 5286) *********************** REFINEMENT MACRO_CYCLE 7 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 185 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 29 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8081 (mmm160) REVERT: K 35 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8683 (tp40) REVERT: K 51 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8030 (mtp-110) REVERT: K 75 ASP cc_start: 0.9046 (t70) cc_final: 0.8762 (t0) REVERT: K 114 MET cc_start: 0.8375 (mmp) cc_final: 0.8157 (mmm) REVERT: K 203 ASN cc_start: 0.8878 (m-40) cc_final: 0.8391 (m-40) REVERT: K 223 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8389 (mt-10) REVERT: K 235 LEU cc_start: 0.8995 (tp) cc_final: 0.7816 (mt) REVERT: K 262 PHE cc_start: 0.8542 (m-80) cc_final: 0.8056 (m-80) REVERT: K 264 CYS cc_start: 0.9173 (t) cc_final: 0.8734 (t) REVERT: K 483 LYS cc_start: 0.9272 (tppp) cc_final: 0.9020 (tmtt) REVERT: K 492 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8345 (tm-30) REVERT: K 493 LEU cc_start: 0.9570 (mt) cc_final: 0.9153 (mt) REVERT: K 494 PHE cc_start: 0.8433 (m-10) cc_final: 0.7890 (m-80) REVERT: K 496 THR cc_start: 0.8682 (t) cc_final: 0.8321 (t) REVERT: K 511 TYR cc_start: 0.8488 (t80) cc_final: 0.7885 (t80) REVERT: K 514 TYR cc_start: 0.8104 (m-80) cc_final: 0.7807 (m-80) REVERT: K 518 THR cc_start: 0.8856 (t) cc_final: 0.8599 (t) REVERT: K 545 THR cc_start: 0.8835 (t) cc_final: 0.8345 (t) REVERT: K 546 LEU cc_start: 0.8254 (tp) cc_final: 0.8003 (tp) REVERT: K 554 GLU cc_start: 0.9504 (tp30) cc_final: 0.9119 (tm-30) REVERT: K 570 ARG cc_start: 0.8965 (tpm170) cc_final: 0.8404 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0661 time to fit residues: 14.8036 Evaluate side-chains 161 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 260 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 337 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 453 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 451 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 ASN ** 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 = 0.3736 r_free = 0.3736 target = 0.129457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109542 restraints weight = 8931.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112630 restraints weight = 5626.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114833 restraints weight = 3981.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116436 restraints weight = 3033.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117615 restraints weight = 2438.826| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 40068 Z= 0.172 Angle : 0.822 11.095 54432 Z= 0.430 Chirality : 0.051 0.181 6264 Planarity : 0.006 0.058 6840 Dihedral : 5.329 20.248 5412 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.23 (0.11), residues: 4788 helix: -0.76 (0.10), residues: 2592 sheet: -0.36 (0.25), residues: 264 loop : -2.61 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 140 TYR 0.018 0.002 TYR I 40 PHE 0.017 0.002 PHE C 31 TRP 0.014 0.002 TRP G 489 HIS 0.007 0.001 HIS F 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (40068) covalent geometry : angle 0.82204 / 0.43 (54432) hydrogen bonds : bond 0.06181 / 4.01 ( 1822) hydrogen bonds : angle 5.90962 / 4.12 ( 5286) *********************** REFINEMENT MACRO_CYCLE 8 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 173 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8473 (mmm160) REVERT: G 31 PHE cc_start: 0.8781 (m-80) cc_final: 0.8151 (m-80) REVERT: G 35 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8572 (tp40) REVERT: G 40 TYR cc_start: 0.8057 (t80) cc_final: 0.7811 (t80) REVERT: G 49 ASN cc_start: 0.8892 (t0) cc_final: 0.7846 (m110) REVERT: G 75 ASP cc_start: 0.9121 (t70) cc_final: 0.8912 (t0) REVERT: G 80 ASP cc_start: 0.8766 (t0) cc_final: 0.8349 (t0) REVERT: G 150 MET cc_start: 0.6174 (mmm) cc_final: 0.5492 (mmm) REVERT: G 197 GLU cc_start: 0.9505 (mp0) cc_final: 0.9269 (mp0) REVERT: G 199 ILE cc_start: 0.9241 (tp) cc_final: 0.9034 (tp) REVERT: G 203 ASN cc_start: 0.8792 (m-40) cc_final: 0.8307 (m-40) REVERT: G 264 CYS cc_start: 0.9139 (t) cc_final: 0.8817 (t) REVERT: G 270 HIS cc_start: 0.8813 (t-90) cc_final: 0.8458 (t-90) REVERT: G 458 ARG cc_start: 0.7267 (tmt170) cc_final: 0.6696 (tmt170) REVERT: G 479 ARG cc_start: 0.8599 (tmt170) cc_final: 0.8251 (ttp80) REVERT: G 483 LYS cc_start: 0.9282 (tppp) cc_final: 0.8928 (tmtt) REVERT: G 493 LEU cc_start: 0.9564 (mt) cc_final: 0.9145 (mt) REVERT: G 496 THR cc_start: 0.8729 (t) cc_final: 0.8405 (t) REVERT: G 511 TYR cc_start: 0.8438 (t80) cc_final: 0.7888 (t80) REVERT: G 518 THR cc_start: 0.8965 (t) cc_final: 0.8717 (t) REVERT: G 526 PHE cc_start: 0.9292 (t80) cc_final: 0.9001 (t80) REVERT: G 545 THR cc_start: 0.8923 (t) cc_final: 0.8471 (t) REVERT: G 546 LEU cc_start: 0.8257 (tp) cc_final: 0.8028 (tp) REVERT: G 554 GLU cc_start: 0.9459 (tp30) cc_final: 0.9116 (tm-30) REVERT: G 570 ARG cc_start: 0.8833 (tpm170) cc_final: 0.8370 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0602 time to fit residues: 12.8119 Evaluate side-chains 163 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 4.9990 chunk 323 optimal weight: 0.0670 chunk 14 optimal weight: 0.2980 chunk 246 optimal weight: 8.9990 chunk 101 optimal weight: 0.0770 chunk 413 optimal weight: 0.0570 chunk 388 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 = 0.3801 r_free = 0.3801 target = 0.133474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112185 restraints weight = 8449.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115287 restraints weight = 5556.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117591 restraints weight = 4029.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119303 restraints weight = 3122.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120642 restraints weight = 2527.862| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40068 Z= 0.157 Angle : 0.824 10.687 54432 Z= 0.426 Chirality : 0.049 0.191 6264 Planarity : 0.006 0.059 6840 Dihedral : 5.272 20.348 5412 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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: -2.19 (0.11), residues: 4788 helix: -0.74 (0.10), residues: 2580 sheet: -0.09 (0.27), residues: 264 loop : -2.61 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 140 TYR 0.024 0.002 TYR K 192 PHE 0.019 0.002 PHE L 494 TRP 0.014 0.001 TRP A 489 HIS 0.007 0.001 HIS F 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (40068) covalent geometry : angle 0.82390 / 0.43 (54432) hydrogen bonds : bond 0.06041 / 3.92 ( 1822) hydrogen bonds : angle 5.79771 / 4.04 ( 5286) *********************** REFINEMENT MACRO_CYCLE 9 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 181 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 PHE cc_start: 0.8796 (m-80) cc_final: 0.8344 (m-80) REVERT: F 35 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8432 (tp40) REVERT: F 49 ASN cc_start: 0.8857 (t0) cc_final: 0.8022 (m110) REVERT: F 50 LEU cc_start: 0.9322 (pt) cc_final: 0.8419 (pt) REVERT: F 71 HIS cc_start: 0.7058 (t-170) cc_final: 0.6723 (t-170) REVERT: F 79 HIS cc_start: 0.8887 (p-80) cc_final: 0.8553 (p90) REVERT: F 80 ASP cc_start: 0.8639 (t0) cc_final: 0.8302 (t0) REVERT: F 81 TRP cc_start: 0.7809 (t60) cc_final: 0.7148 (t60) REVERT: F 92 TRP cc_start: 0.8255 (t-100) cc_final: 0.8028 (t-100) REVERT: F 107 PHE cc_start: 0.9113 (t80) cc_final: 0.8826 (t80) REVERT: F 135 VAL cc_start: 0.9383 (p) cc_final: 0.8998 (p) REVERT: F 140 ARG cc_start: 0.9171 (mtp85) cc_final: 0.8830 (mmm-85) REVERT: F 193 GLU cc_start: 0.9209 (mp0) cc_final: 0.8786 (pm20) REVERT: F 197 GLU cc_start: 0.9463 (mp0) cc_final: 0.9242 (mp0) REVERT: F 209 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7965 (tm-30) REVERT: F 225 VAL cc_start: 0.7487 (p) cc_final: 0.7285 (t) REVERT: F 235 LEU cc_start: 0.9013 (tp) cc_final: 0.8225 (mm) REVERT: F 270 HIS cc_start: 0.8983 (t-90) cc_final: 0.8339 (t-90) REVERT: F 455 LEU cc_start: 0.8757 (tp) cc_final: 0.8517 (tp) REVERT: F 458 ARG cc_start: 0.7365 (tmt170) cc_final: 0.7074 (tmt170) REVERT: F 481 MET cc_start: 0.9126 (tpp) cc_final: 0.8513 (tpp) REVERT: F 483 LYS cc_start: 0.9289 (tppp) cc_final: 0.8908 (tmtt) REVERT: F 511 TYR cc_start: 0.8351 (t80) cc_final: 0.7790 (t80) REVERT: F 514 TYR cc_start: 0.8122 (m-80) cc_final: 0.7833 (m-80) REVERT: F 526 PHE cc_start: 0.9060 (t80) cc_final: 0.8729 (t80) REVERT: F 545 THR cc_start: 0.8865 (t) cc_final: 0.8441 (t) REVERT: F 554 GLU cc_start: 0.9366 (tp30) cc_final: 0.9045 (tm-30) REVERT: F 564 TYR cc_start: 0.8680 (m-10) cc_final: 0.8344 (m-80) REVERT: F 570 ARG cc_start: 0.8898 (tpm170) cc_final: 0.8417 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0672 time to fit residues: 14.7636 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 : 0.129 ------------------------------------------------------------------------------- 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: 7.9990 chunk 375 optimal weight: 0.0050 chunk 420 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 184 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 73 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 overall best weight: 0.6612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 49 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 HIS ** F 255 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 = 0.3815 r_free = 0.3815 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113946 restraints weight = 8474.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117044 restraints weight = 5564.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119377 restraints weight = 4025.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121132 restraints weight = 3097.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122195 restraints weight = 2508.021| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.8328 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= 0.174 Angle : 0.861 9.275 54432 Z= 0.453 Chirality : 0.052 0.181 6264 Planarity : 0.006 0.061 6840 Dihedral : 5.340 20.632 5412 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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: -2.16 (0.11), residues: 4788 helix: -0.70 (0.10), residues: 2460 sheet: -0.02 (0.27), residues: 264 loop : -2.54 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 140 TYR 0.013 0.002 TYR E 258 PHE 0.032 0.002 PHE H 494 TRP 0.015 0.001 TRP G 489 HIS 0.008 0.002 HIS F 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (40068) covalent geometry : angle 0.86109 / 0.45 (54432) hydrogen bonds : bond 0.06118 / 3.97 ( 1822) hydrogen bonds : angle 5.87100 / 4.08 ( 5286) ********************** REFINEMENT MACRO_CYCLE 10 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 175 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 PHE cc_start: 0.8875 (m-80) cc_final: 0.8583 (m-80) REVERT: F 49 ASN cc_start: 0.8897 (t160) cc_final: 0.8129 (m110) REVERT: F 61 PHE cc_start: 0.9130 (t80) cc_final: 0.8885 (t80) REVERT: F 80 ASP cc_start: 0.8656 (t0) cc_final: 0.8289 (t0) REVERT: F 81 TRP cc_start: 0.7880 (t60) cc_final: 0.7102 (t60) REVERT: F 87 CYS cc_start: 0.8862 (t) cc_final: 0.8575 (p) REVERT: F 92 TRP cc_start: 0.8369 (t-100) cc_final: 0.8116 (t-100) REVERT: F 107 PHE cc_start: 0.9137 (t80) cc_final: 0.8864 (t80) REVERT: F 140 ARG cc_start: 0.9161 (mtp85) cc_final: 0.8812 (mmm-85) REVERT: F 150 MET cc_start: 0.6647 (mmm) cc_final: 0.5746 (mmm) REVERT: F 193 GLU cc_start: 0.9197 (mp0) cc_final: 0.8779 (pm20) REVERT: F 197 GLU cc_start: 0.9493 (mp0) cc_final: 0.9241 (mp0) REVERT: F 223 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8027 (mt-10) REVERT: F 232 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8820 (ttm-80) REVERT: F 235 LEU cc_start: 0.9092 (tp) cc_final: 0.8291 (mm) REVERT: F 270 HIS cc_start: 0.8910 (t-90) cc_final: 0.8448 (t-90) REVERT: F 458 ARG cc_start: 0.7343 (tmt170) cc_final: 0.7059 (tmt170) REVERT: F 481 MET cc_start: 0.9191 (tpp) cc_final: 0.8762 (tpp) REVERT: F 483 LYS cc_start: 0.9371 (tppp) cc_final: 0.8805 (tmtt) REVERT: F 511 TYR cc_start: 0.8401 (t80) cc_final: 0.7805 (t80) REVERT: F 514 TYR cc_start: 0.8057 (m-80) cc_final: 0.7801 (m-80) REVERT: F 526 PHE cc_start: 0.9018 (t80) cc_final: 0.8663 (t80) REVERT: F 545 THR cc_start: 0.8850 (t) cc_final: 0.8353 (t) REVERT: F 546 LEU cc_start: 0.8412 (tp) cc_final: 0.7453 (tp) REVERT: F 550 GLU cc_start: 0.9496 (mm-30) cc_final: 0.8517 (tp30) REVERT: F 554 GLU cc_start: 0.9342 (tp30) cc_final: 0.9029 (tm-30) REVERT: F 564 TYR cc_start: 0.8692 (m-10) cc_final: 0.8337 (m-80) REVERT: F 570 ARG cc_start: 0.8904 (tpm170) cc_final: 0.8412 (ttp80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0690 time to fit residues: 14.5149 Evaluate side-chains 153 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 7.9990 chunk 404 optimal weight: 0.4980 chunk 417 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 424 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 chunk 395 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 399 optimal weight: 0.1980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 49 ASN F 71 HIS F 82 ASN F 163 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112836 restraints weight = 8663.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116038 restraints weight = 5669.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118451 restraints weight = 4109.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120089 restraints weight = 3173.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121285 restraints weight = 2595.579| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40068 Z= 0.169 Angle : 0.830 9.114 54432 Z= 0.435 Chirality : 0.050 0.171 6264 Planarity : 0.005 0.059 6840 Dihedral : 5.240 19.236 5412 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 21.04 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: -2.13 (0.11), residues: 4788 helix: -0.67 (0.10), residues: 2568 sheet: 0.01 (0.27), residues: 264 loop : -2.62 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 509 TYR 0.012 0.002 TYR H 224 PHE 0.022 0.002 PHE E 494 TRP 0.019 0.001 TRP I 489 HIS 0.007 0.002 HIS F 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (40068) covalent geometry : angle 0.83036 / 0.44 (54432) hydrogen bonds : bond 0.05929 / 3.87 ( 1822) hydrogen bonds : angle 5.74102 / 3.99 ( 5286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.71 seconds wall clock time: 44 minutes 48.23 seconds (2688.23 seconds total)