Starting phenix.real_space_refine on Sat Mar 7 05:46:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4m_25680/03_2026/7t4m_25680.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.039 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 264 5.16 5 C 25002 2.51 5 N 6576 2.21 5 O 7212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39054 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "B" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "C" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "D" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "E" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "F" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "G" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "H" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "I" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "J" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "K" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "L" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Time building chain proxies: 14.29, per 1000 atoms: 0.37 Number of scatterers: 39054 At special positions: 0 Unit cell: (164.101, 162.435, 124.117, 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 264 16.00 O 7212 8.00 N 6576 7.00 C 25002 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: 3.64 Conformation dependent library (CDL) restraints added in 3.4 seconds 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9444 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 45.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.631A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.529A pdb=" N CYS A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS A 512 " --> pdb=" O CYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.396A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS B 360 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 414 " --> pdb=" O TRP B 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 557 through 574 Processing helix chain 'C' and resid 119 through 137 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS C 360 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 Processing helix chain 'C' and resid 406 through 420 removed outlier: 3.532A pdb=" N ALA C 414 " --> pdb=" O TRP C 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 471 through 485 Processing helix chain 'C' and resid 486 through 491 removed outlier: 3.769A pdb=" N LEU C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS C 512 " --> pdb=" O CYS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 554 Processing helix chain 'C' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS C 572 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS D 328 " --> pdb=" O HIS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 removed outlier: 4.466A pdb=" N CYS D 360 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 Processing helix chain 'D' and resid 406 through 420 removed outlier: 3.598A pdb=" N GLY D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 414 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 417 " --> pdb=" O GLY D 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 542 through 554 Processing helix chain 'D' and resid 557 through 574 Processing helix chain 'E' and resid 119 through 137 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS E 328 " --> pdb=" O HIS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 357 through 361 removed outlier: 4.527A pdb=" N CYS E 360 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'E' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA E 414 " --> pdb=" O TRP E 410 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 471 through 485 Processing helix chain 'E' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU E 490 " --> pdb=" O PRO E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS E 512 " --> pdb=" O CYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 554 Processing helix chain 'E' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS E 572 " --> pdb=" O ILE E 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 155 through 159 Processing helix chain 'F' and resid 203 through 215 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 307 through 328 removed outlier: 3.635A pdb=" N HIS F 328 " --> pdb=" O HIS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS F 360 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 406 through 420 removed outlier: 3.598A pdb=" N GLY F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 414 " --> pdb=" O TRP F 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 486 through 491 removed outlier: 3.572A pdb=" N LEU F 490 " --> pdb=" O PRO F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 516 Processing helix chain 'F' and resid 542 through 554 Processing helix chain 'F' and resid 557 through 574 Processing helix chain 'G' and resid 119 through 137 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 203 through 215 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 307 through 328 removed outlier: 3.631A pdb=" N HIS G 328 " --> pdb=" O HIS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS G 360 " --> pdb=" O ALA G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 393 Processing helix chain 'G' and resid 406 through 420 removed outlier: 3.532A pdb=" N ALA G 414 " --> pdb=" O TRP G 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 417 " --> pdb=" O GLY G 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 462 Processing helix chain 'G' and resid 471 through 485 Processing helix chain 'G' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU G 490 " --> pdb=" O PRO G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS G 512 " --> pdb=" O CYS G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 554 Processing helix chain 'G' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS G 572 " --> pdb=" O ILE G 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY H 126 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS H 328 " --> pdb=" O HIS H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS H 360 " --> pdb=" O ALA H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 393 Processing helix chain 'H' and resid 406 through 420 removed outlier: 3.599A pdb=" N GLY H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 414 " --> pdb=" O TRP H 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 417 " --> pdb=" O GLY H 413 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 462 Processing helix chain 'H' and resid 471 through 485 Processing helix chain 'H' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU H 490 " --> pdb=" O PRO H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 516 Processing helix chain 'H' and resid 542 through 554 Processing helix chain 'H' and resid 557 through 574 Processing helix chain 'I' and resid 119 through 137 Processing helix chain 'I' and resid 148 through 152 Processing helix chain 'I' and resid 155 through 159 Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS I 328 " --> pdb=" O HIS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 338 No H-bonds generated for 'chain 'I' and resid 336 through 338' Processing helix chain 'I' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS I 360 " --> pdb=" O ALA I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 393 Processing helix chain 'I' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA I 414 " --> pdb=" O TRP I 410 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 417 " --> pdb=" O GLY I 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU I 418 " --> pdb=" O ALA I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 471 through 485 Processing helix chain 'I' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU I 490 " --> pdb=" O PRO I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS I 512 " --> pdb=" O CYS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 554 Processing helix chain 'I' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS I 572 " --> pdb=" O ILE I 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 152 Processing helix chain 'J' and resid 155 through 159 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS J 328 " --> pdb=" O HIS J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS J 360 " --> pdb=" O ALA J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 393 Processing helix chain 'J' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY J 413 " --> pdb=" O LEU J 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 414 " --> pdb=" O TRP J 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR J 417 " --> pdb=" O GLY J 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 462 Processing helix chain 'J' and resid 471 through 485 Processing helix chain 'J' and resid 486 through 491 removed outlier: 3.572A pdb=" N LEU J 490 " --> pdb=" O PRO J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 516 Processing helix chain 'J' and resid 542 through 554 Processing helix chain 'J' and resid 557 through 574 Processing helix chain 'K' and resid 119 through 137 Processing helix chain 'K' and resid 148 through 152 Processing helix chain 'K' and resid 155 through 159 Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS K 328 " --> pdb=" O HIS K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 338 No H-bonds generated for 'chain 'K' and resid 336 through 338' Processing helix chain 'K' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS K 360 " --> pdb=" O ALA K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'K' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA K 414 " --> pdb=" O TRP K 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 417 " --> pdb=" O GLY K 413 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU K 418 " --> pdb=" O ALA K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 462 Processing helix chain 'K' and resid 471 through 485 Processing helix chain 'K' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU K 490 " --> pdb=" O PRO K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS K 512 " --> pdb=" O CYS K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 542 through 554 Processing helix chain 'K' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS K 572 " --> pdb=" O ILE K 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 155 through 159 Processing helix chain 'L' and resid 203 through 215 Processing helix chain 'L' and resid 297 through 304 Processing helix chain 'L' and resid 307 through 328 removed outlier: 3.635A pdb=" N HIS L 328 " --> pdb=" O HIS L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 361 removed outlier: 4.466A pdb=" N CYS L 360 " --> pdb=" O ALA L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 393 Processing helix chain 'L' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA L 414 " --> pdb=" O TRP L 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR L 417 " --> pdb=" O GLY L 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU L 418 " --> pdb=" O ALA L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 462 Processing helix chain 'L' and resid 471 through 485 Processing helix chain 'L' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU L 490 " --> pdb=" O PRO L 486 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 516 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 557 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS A 295 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 254 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 372 Processing sheet with id=AA9, first strand: chain 'C' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER C 251 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS C 291 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET C 249 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 254 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS C 295 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AB3, first strand: chain 'C' and resid 370 through 372 Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER D 251 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS D 291 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET D 249 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 254 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AB6, first strand: chain 'D' and resid 330 through 331 Processing sheet with id=AB7, first strand: chain 'D' and resid 370 through 372 Processing sheet with id=AB8, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER E 251 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS E 291 " --> pdb=" O MET E 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET E 249 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 254 " --> pdb=" O PHE E 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS E 295 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'E' and resid 370 through 372 Processing sheet with id=AC3, first strand: chain 'F' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER F 251 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS F 291 " --> pdb=" O MET F 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET F 249 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 254 " --> pdb=" O PHE F 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 295 through 296 Processing sheet with id=AC5, first strand: chain 'F' and resid 330 through 331 Processing sheet with id=AC6, first strand: chain 'F' and resid 370 through 372 Processing sheet with id=AC7, first strand: chain 'G' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER G 251 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS G 291 " --> pdb=" O MET G 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET G 249 " --> pdb=" O LYS G 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 254 " --> pdb=" O PHE G 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS G 295 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 330 through 331 Processing sheet with id=AD1, first strand: chain 'G' and resid 370 through 372 Processing sheet with id=AD2, first strand: chain 'H' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER H 251 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS H 291 " --> pdb=" O MET H 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET H 249 " --> pdb=" O LYS H 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 254 " --> pdb=" O PHE H 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AD4, first strand: chain 'H' and resid 330 through 331 Processing sheet with id=AD5, first strand: chain 'H' and resid 370 through 372 Processing sheet with id=AD6, first strand: chain 'I' and resid 165 through 166 removed outlier: 3.540A pdb=" N SER I 251 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS I 291 " --> pdb=" O MET I 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET I 249 " --> pdb=" O LYS I 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 254 " --> pdb=" O PHE I 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS I 295 " --> pdb=" O VAL I 342 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 330 through 331 Processing sheet with id=AD9, first strand: chain 'I' and resid 370 through 372 Processing sheet with id=AE1, first strand: chain 'J' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER J 251 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS J 291 " --> pdb=" O MET J 249 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET J 249 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 254 " --> pdb=" O PHE J 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 295 through 296 Processing sheet with id=AE3, first strand: chain 'J' and resid 330 through 331 Processing sheet with id=AE4, first strand: chain 'J' and resid 370 through 372 Processing sheet with id=AE5, first strand: chain 'K' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER K 251 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS K 291 " --> pdb=" O MET K 249 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET K 249 " --> pdb=" O LYS K 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA K 254 " --> pdb=" O PHE K 222 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS K 295 " --> pdb=" O VAL K 342 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 330 through 331 Processing sheet with id=AE8, first strand: chain 'K' and resid 370 through 372 Processing sheet with id=AE9, first strand: chain 'L' and resid 165 through 167 removed outlier: 3.590A pdb=" N SER L 251 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS L 291 " --> pdb=" O MET L 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET L 249 " --> pdb=" O LYS L 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA L 254 " --> pdb=" O PHE L 222 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 295 through 296 Processing sheet with id=AF2, first strand: chain 'L' and resid 330 through 331 Processing sheet with id=AF3, first strand: chain 'L' and resid 370 through 372 1770 hydrogen bonds defined for protein. 4920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.49 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12606 1.34 - 1.46: 8664 1.46 - 1.58: 18162 1.58 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 39840 Sorted by residual: bond pdb=" C GLU F 346 " pdb=" N GLY F 347 " ideal model delta sigma weight residual 1.321 1.331 -0.009 1.24e-02 6.50e+03 5.55e-01 bond pdb=" C GLU B 346 " pdb=" N GLY B 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.34e-01 bond pdb=" C GLU H 346 " pdb=" N GLY H 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.23e-01 bond pdb=" C GLU J 346 " pdb=" N GLY J 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.05e-01 bond pdb=" C GLU D 346 " pdb=" N GLY D 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 4.98e-01 ... (remaining 39835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 52616 0.94 - 1.88: 995 1.88 - 2.82: 249 2.82 - 3.77: 74 3.77 - 4.71: 12 Bond angle restraints: 53946 Sorted by residual: angle pdb=" N ILE L 257 " pdb=" CA ILE L 257 " pdb=" C ILE L 257 " ideal model delta sigma weight residual 107.60 109.64 -2.04 1.07e+00 8.73e-01 3.65e+00 angle pdb=" N ILE B 257 " pdb=" CA ILE B 257 " pdb=" C ILE B 257 " ideal model delta sigma weight residual 107.60 109.62 -2.02 1.07e+00 8.73e-01 3.56e+00 angle pdb=" N ILE F 257 " pdb=" CA ILE F 257 " pdb=" C ILE F 257 " ideal model delta sigma weight residual 107.60 109.62 -2.02 1.07e+00 8.73e-01 3.55e+00 angle pdb=" N ILE H 257 " pdb=" CA ILE H 257 " pdb=" C ILE H 257 " ideal model delta sigma weight residual 107.60 109.60 -2.00 1.07e+00 8.73e-01 3.49e+00 angle pdb=" N ILE D 257 " pdb=" CA ILE D 257 " pdb=" C ILE D 257 " ideal model delta sigma weight residual 107.60 109.57 -1.97 1.07e+00 8.73e-01 3.39e+00 ... (remaining 53941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 23448 17.61 - 35.21: 798 35.21 - 52.82: 102 52.82 - 70.42: 42 70.42 - 88.03: 24 Dihedral angle restraints: 24414 sinusoidal: 9930 harmonic: 14484 Sorted by residual: dihedral pdb=" CB GLU G 123 " pdb=" CG GLU G 123 " pdb=" CD GLU G 123 " pdb=" OE1 GLU G 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.03 -88.03 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " pdb=" CD GLU C 123 " pdb=" OE1 GLU C 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.02 -88.02 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU E 123 " pdb=" CG GLU E 123 " pdb=" CD GLU E 123 " pdb=" OE1 GLU E 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.01 -88.01 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 24411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3970 0.029 - 0.057: 1478 0.057 - 0.086: 360 0.086 - 0.114: 218 0.114 - 0.143: 58 Chirality restraints: 6084 Sorted by residual: chirality pdb=" CA ILE J 450 " pdb=" N ILE J 450 " pdb=" C ILE J 450 " pdb=" CB ILE J 450 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE L 450 " pdb=" N ILE L 450 " pdb=" C ILE L 450 " pdb=" CB ILE L 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 6081 not shown) Planarity restraints: 6846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 450 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO K 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO K 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO K 451 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 450 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO I 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 451 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 450 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " -0.018 5.00e-02 4.00e+02 ... (remaining 6843 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7896 2.78 - 3.31: 37699 3.31 - 3.84: 65046 3.84 - 4.37: 81568 4.37 - 4.90: 137599 Nonbonded interactions: 329808 Sorted by model distance: nonbonded pdb=" O THR G 215 " pdb=" OH TYR G 221 " model vdw 2.253 3.040 nonbonded pdb=" O THR A 215 " pdb=" OH TYR A 221 " model vdw 2.253 3.040 nonbonded pdb=" O THR K 215 " pdb=" OH TYR K 221 " model vdw 2.254 3.040 nonbonded pdb=" O THR E 215 " pdb=" OH TYR E 221 " model vdw 2.254 3.040 nonbonded pdb=" O THR I 215 " pdb=" OH TYR I 221 " model vdw 2.254 3.040 ... (remaining 329803 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 47.260 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.001 0.026 39840 Z= 0.071 Angle : 0.375 4.708 53946 Z= 0.198 Chirality : 0.036 0.143 6084 Planarity : 0.003 0.033 6846 Dihedral : 9.690 88.027 14970 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 3.90 % Favored : 95.13 % 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: 1.34 (0.12), residues: 4746 helix: 1.99 (0.12), residues: 1896 sheet: -0.21 (0.18), residues: 786 loop : 0.42 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 384 TYR 0.006 0.001 TYR A 174 PHE 0.006 0.001 PHE F 196 TRP 0.007 0.001 TRP J 484 HIS 0.002 0.000 HIS J 572 Details of bonding type rmsd covalent geometry : bond 0.00143 (39840) covalent geometry : angle 0.37512 (53946) hydrogen bonds : bond 0.23983 ( 1770) hydrogen bonds : angle 6.54884 ( 4920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 641 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 195 MET cc_start: 0.8396 (mtp) cc_final: 0.8111 (mtm) REVERT: A 441 GLU cc_start: 0.7646 (mp0) cc_final: 0.7441 (mt-10) REVERT: C 189 GLN cc_start: 0.6366 (tp40) cc_final: 0.6152 (tp-100) REVERT: C 441 GLU cc_start: 0.7602 (mp0) cc_final: 0.7341 (mp0) REVERT: D 160 ASP cc_start: 0.7265 (t70) cc_final: 0.7029 (t0) REVERT: D 167 LYS cc_start: 0.7883 (tppt) cc_final: 0.7632 (mmtp) REVERT: D 302 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: E 195 MET cc_start: 0.8286 (mtp) cc_final: 0.8032 (mtm) REVERT: E 209 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7671 (ttpt) REVERT: E 441 GLU cc_start: 0.7616 (mp0) cc_final: 0.7401 (mt-10) REVERT: F 167 LYS cc_start: 0.7874 (tppt) cc_final: 0.7658 (mmtm) REVERT: F 195 MET cc_start: 0.8684 (mtp) cc_final: 0.8465 (mtm) REVERT: F 302 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: G 195 MET cc_start: 0.8278 (mtp) cc_final: 0.8077 (mtp) REVERT: G 431 MET cc_start: 0.7347 (mmt) cc_final: 0.7078 (mmt) REVERT: G 441 GLU cc_start: 0.7574 (mp0) cc_final: 0.7301 (mp0) REVERT: H 160 ASP cc_start: 0.7330 (t70) cc_final: 0.7063 (t0) REVERT: H 167 LYS cc_start: 0.7885 (tppt) cc_final: 0.7664 (mmtp) REVERT: H 302 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7744 (ttp-170) REVERT: I 195 MET cc_start: 0.8271 (mtp) cc_final: 0.8061 (mtm) REVERT: J 302 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7723 (ttp-170) REVERT: K 209 LYS cc_start: 0.8009 (ttpp) cc_final: 0.7676 (ttpt) REVERT: K 441 GLU cc_start: 0.7646 (mp0) cc_final: 0.7434 (mt-10) REVERT: L 195 MET cc_start: 0.8663 (mtp) cc_final: 0.8462 (mtm) outliers start: 42 outliers final: 8 residues processed: 652 average time/residue: 0.8156 time to fit residues: 628.8645 Evaluate side-chains 532 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 524 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain L residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.0770 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN A 504 GLN B 197 ASN B 366 GLN C 152 GLN C 170 ASN D 366 GLN D 559 HIS E 170 ASN E 189 GLN F 197 ASN F 224 ASN F 504 GLN F 559 HIS G 152 GLN G 170 ASN G 189 GLN H 197 ASN H 366 GLN H 504 GLN H 559 HIS I 170 ASN I 189 GLN J 197 ASN J 224 ASN J 559 HIS K 152 GLN K 170 ASN K 189 GLN L 197 ASN L 366 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111586 restraints weight = 94445.261| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.70 r_work: 0.3207 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39840 Z= 0.117 Angle : 0.502 6.281 53946 Z= 0.264 Chirality : 0.040 0.136 6084 Planarity : 0.004 0.034 6846 Dihedral : 3.574 26.210 5288 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.69 % Allowed : 7.50 % Favored : 91.81 % 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: 1.58 (0.12), residues: 4746 helix: 2.18 (0.11), residues: 2016 sheet: -0.07 (0.18), residues: 756 loop : 0.43 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 309 TYR 0.012 0.001 TYR H 482 PHE 0.013 0.001 PHE L 452 TRP 0.008 0.001 TRP A 129 HIS 0.004 0.001 HIS C 572 Details of bonding type rmsd covalent geometry : bond 0.00254 (39840) covalent geometry : angle 0.50242 (53946) hydrogen bonds : bond 0.05300 ( 1770) hydrogen bonds : angle 5.00314 ( 4920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 570 time to evaluate : 1.537 Fit side-chains REVERT: A 428 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: B 160 ASP cc_start: 0.7622 (t70) cc_final: 0.7288 (t70) REVERT: B 366 GLN cc_start: 0.8764 (mt0) cc_final: 0.8507 (mt0) REVERT: C 441 GLU cc_start: 0.7799 (mp0) cc_final: 0.7453 (mp0) REVERT: D 123 GLU cc_start: 0.7799 (mp0) cc_final: 0.7542 (mp0) REVERT: D 160 ASP cc_start: 0.7551 (t70) cc_final: 0.7227 (t70) REVERT: D 167 LYS cc_start: 0.7688 (mppt) cc_final: 0.7347 (mmtp) REVERT: D 302 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7730 (ttp-170) REVERT: E 209 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7853 (ttpt) REVERT: E 441 GLU cc_start: 0.7825 (mp0) cc_final: 0.7396 (mp0) REVERT: F 160 ASP cc_start: 0.7627 (t70) cc_final: 0.7340 (t70) REVERT: F 302 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7798 (ttp-170) REVERT: G 441 GLU cc_start: 0.7775 (mp0) cc_final: 0.7399 (mp0) REVERT: G 492 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7620 (tp30) REVERT: H 123 GLU cc_start: 0.7812 (mp0) cc_final: 0.7565 (mp0) REVERT: H 160 ASP cc_start: 0.7574 (t70) cc_final: 0.7197 (t70) REVERT: H 302 ARG cc_start: 0.8068 (ttp-170) cc_final: 0.7811 (ttp-170) REVERT: J 160 ASP cc_start: 0.7671 (t70) cc_final: 0.7359 (t70) REVERT: J 302 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7827 (ttp-170) REVERT: K 428 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: L 160 ASP cc_start: 0.7536 (t70) cc_final: 0.7171 (t70) REVERT: L 366 GLN cc_start: 0.8663 (mt0) cc_final: 0.8389 (mt0) outliers start: 30 outliers final: 12 residues processed: 586 average time/residue: 0.7461 time to fit residues: 522.3151 Evaluate side-chains 530 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 516 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 235 ASP Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 428 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 422 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 chunk 318 optimal weight: 0.7980 chunk 383 optimal weight: 5.9990 chunk 120 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 504 GLN B 197 ASN C 152 GLN C 189 GLN C 366 GLN C 572 HIS D 366 GLN D 559 HIS E 152 GLN E 189 GLN E 504 GLN F 197 ASN F 224 ASN G 152 GLN G 189 GLN H 366 GLN H 559 HIS I 152 GLN I 189 GLN J 197 ASN J 224 ASN K 152 GLN K 189 GLN L 197 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111167 restraints weight = 87627.027| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.57 r_work: 0.3208 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39840 Z= 0.102 Angle : 0.461 5.767 53946 Z= 0.240 Chirality : 0.039 0.132 6084 Planarity : 0.004 0.037 6846 Dihedral : 3.499 13.962 5274 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.99 % Allowed : 8.45 % Favored : 90.56 % 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: 1.57 (0.12), residues: 4746 helix: 2.21 (0.11), residues: 2028 sheet: 0.14 (0.18), residues: 660 loop : 0.26 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 292 TYR 0.011 0.001 TYR A 482 PHE 0.014 0.001 PHE D 452 TRP 0.007 0.001 TRP E 505 HIS 0.003 0.001 HIS F 572 Details of bonding type rmsd covalent geometry : bond 0.00224 (39840) covalent geometry : angle 0.46090 (53946) hydrogen bonds : bond 0.04343 ( 1770) hydrogen bonds : angle 4.61600 ( 4920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 557 time to evaluate : 1.498 Fit side-chains REVERT: A 428 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: B 123 GLU cc_start: 0.8173 (mp0) cc_final: 0.7910 (mp0) REVERT: B 160 ASP cc_start: 0.7799 (t70) cc_final: 0.7470 (OUTLIER) REVERT: B 431 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: C 195 MET cc_start: 0.8948 (mtp) cc_final: 0.8723 (mtp) REVERT: C 284 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.6644 (tmt) REVERT: C 441 GLU cc_start: 0.7852 (mp0) cc_final: 0.7451 (mp0) REVERT: D 123 GLU cc_start: 0.7922 (mp0) cc_final: 0.7520 (mp0) REVERT: D 160 ASP cc_start: 0.7728 (t70) cc_final: 0.7410 (t70) REVERT: D 167 LYS cc_start: 0.7747 (tppt) cc_final: 0.7328 (mppt) REVERT: D 302 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7770 (ttp-170) REVERT: E 284 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.5653 (tmt) REVERT: E 441 GLU cc_start: 0.7891 (mp0) cc_final: 0.7474 (mp0) REVERT: F 160 ASP cc_start: 0.7821 (t70) cc_final: 0.7484 (OUTLIER) REVERT: F 255 ASP cc_start: 0.7772 (p0) cc_final: 0.7559 (p0) REVERT: F 302 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7835 (ttp-170) REVERT: F 498 ASN cc_start: 0.8011 (p0) cc_final: 0.7560 (p0) REVERT: G 149 GLU cc_start: 0.5988 (pm20) cc_final: 0.5746 (pm20) REVERT: G 284 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6131 (tmt) REVERT: G 441 GLU cc_start: 0.7891 (mp0) cc_final: 0.7491 (mp0) REVERT: G 492 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7710 (tp30) REVERT: H 123 GLU cc_start: 0.7963 (mp0) cc_final: 0.7763 (mp0) REVERT: H 160 ASP cc_start: 0.7725 (t70) cc_final: 0.7386 (t70) REVERT: H 255 ASP cc_start: 0.7766 (p0) cc_final: 0.7468 (p0) REVERT: H 302 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7876 (ttp-170) REVERT: I 284 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.5149 (tmt) REVERT: J 160 ASP cc_start: 0.7897 (t70) cc_final: 0.7562 (t70) REVERT: J 255 ASP cc_start: 0.7779 (p0) cc_final: 0.7550 (p0) REVERT: J 292 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8168 (tmm-80) REVERT: J 302 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7855 (ttp-170) REVERT: J 498 ASN cc_start: 0.7947 (p0) cc_final: 0.7495 (p0) REVERT: K 189 GLN cc_start: 0.6436 (tp40) cc_final: 0.6232 (tp-100) REVERT: K 428 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: L 160 ASP cc_start: 0.7734 (t70) cc_final: 0.7404 (OUTLIER) outliers start: 43 outliers final: 18 residues processed: 567 average time/residue: 0.7925 time to fit residues: 533.2383 Evaluate side-chains 536 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 514 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 284 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 235 ASP Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 428 ASP Chi-restraints excluded: chain L residue 155 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 314 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 388 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN A 366 GLN B 197 ASN C 152 GLN C 189 GLN C 572 HIS D 366 GLN D 504 GLN E 189 GLN E 504 GLN F 197 ASN F 224 ASN G 152 GLN H 366 GLN I 189 GLN J 197 ASN J 224 ASN K 152 GLN K 170 ASN K 283 ASN K 366 GLN L 197 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106428 restraints weight = 71397.914| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.37 r_work: 0.3148 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39840 Z= 0.176 Angle : 0.541 8.996 53946 Z= 0.281 Chirality : 0.043 0.138 6084 Planarity : 0.004 0.049 6846 Dihedral : 3.968 14.819 5274 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.34 % Allowed : 8.63 % Favored : 90.03 % 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: 1.18 (0.12), residues: 4746 helix: 1.92 (0.11), residues: 2016 sheet: -0.29 (0.18), residues: 690 loop : 0.11 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 292 TYR 0.017 0.002 TYR A 482 PHE 0.020 0.002 PHE B 452 TRP 0.009 0.002 TRP A 489 HIS 0.006 0.001 HIS H 572 Details of bonding type rmsd covalent geometry : bond 0.00420 (39840) covalent geometry : angle 0.54065 (53946) hydrogen bonds : bond 0.04984 ( 1770) hydrogen bonds : angle 4.68788 ( 4920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 530 time to evaluate : 1.526 Fit side-chains REVERT: A 428 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: A 496 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (mm) REVERT: B 160 ASP cc_start: 0.7863 (t70) cc_final: 0.7569 (OUTLIER) REVERT: B 431 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: C 167 LYS cc_start: 0.8077 (tptm) cc_final: 0.7844 (tttt) REVERT: C 284 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.5727 (tmt) REVERT: C 441 GLU cc_start: 0.7901 (mp0) cc_final: 0.7477 (mp0) REVERT: C 496 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7512 (mp) REVERT: D 123 GLU cc_start: 0.8038 (mp0) cc_final: 0.7635 (mp0) REVERT: D 160 ASP cc_start: 0.7871 (t70) cc_final: 0.7579 (t70) REVERT: D 224 ASN cc_start: 0.7923 (t0) cc_final: 0.7646 (t160) REVERT: D 302 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7860 (ttp-170) REVERT: E 195 MET cc_start: 0.9047 (mtp) cc_final: 0.8837 (mtm) REVERT: E 248 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7660 (tpt-90) REVERT: E 496 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7359 (mp) REVERT: F 255 ASP cc_start: 0.7892 (p0) cc_final: 0.7639 (p0) REVERT: G 149 GLU cc_start: 0.6168 (pm20) cc_final: 0.5849 (pm20) REVERT: G 284 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.5822 (tmt) REVERT: G 441 GLU cc_start: 0.7895 (mp0) cc_final: 0.7483 (mp0) REVERT: G 496 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7494 (mp) REVERT: H 123 GLU cc_start: 0.8050 (mp0) cc_final: 0.7642 (mp0) REVERT: H 160 ASP cc_start: 0.7811 (t70) cc_final: 0.7545 (t70) REVERT: H 224 ASN cc_start: 0.7926 (t0) cc_final: 0.7650 (t160) REVERT: H 255 ASP cc_start: 0.7874 (p0) cc_final: 0.7591 (p0) REVERT: H 302 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7884 (ttp-170) REVERT: I 195 MET cc_start: 0.9068 (mtp) cc_final: 0.8833 (mtm) REVERT: I 284 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.4981 (tmt) REVERT: I 471 ASP cc_start: 0.8905 (m-30) cc_final: 0.8674 (m-30) REVERT: I 496 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7347 (mp) REVERT: J 255 ASP cc_start: 0.7862 (p0) cc_final: 0.7602 (p0) REVERT: J 302 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7811 (ttp-170) REVERT: K 189 GLN cc_start: 0.6666 (tp40) cc_final: 0.6366 (tp40) REVERT: K 428 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: K 496 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7902 (mm) REVERT: K 504 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: L 160 ASP cc_start: 0.7842 (t70) cc_final: 0.7550 (OUTLIER) REVERT: L 167 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7592 (mmtm) outliers start: 58 outliers final: 28 residues processed: 548 average time/residue: 0.7925 time to fit residues: 515.8211 Evaluate side-chains 538 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 498 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 573 ILE Chi-restraints excluded: chain I residue 284 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain J residue 235 ASP Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 428 ASP Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 504 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 198 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 453 optimal weight: 10.0000 chunk 359 optimal weight: 0.5980 chunk 205 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 427 optimal weight: 7.9990 chunk 406 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN A 366 GLN A 504 GLN C 152 GLN C 366 GLN C 504 GLN D 366 GLN E 152 GLN E 189 GLN E 504 GLN F 224 ASN F 283 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 504 GLN I 152 GLN J 224 ASN J 283 ASN J 366 GLN K 152 GLN K 170 ASN K 283 ASN K 366 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108591 restraints weight = 79290.428| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.45 r_work: 0.3176 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39840 Z= 0.108 Angle : 0.474 7.916 53946 Z= 0.246 Chirality : 0.039 0.134 6084 Planarity : 0.004 0.046 6846 Dihedral : 3.776 14.126 5274 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.18 % Allowed : 9.16 % Favored : 89.66 % 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: 1.35 (0.12), residues: 4746 helix: 2.16 (0.11), residues: 1992 sheet: -0.11 (0.18), residues: 660 loop : 0.07 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 292 TYR 0.011 0.001 TYR A 482 PHE 0.012 0.001 PHE D 452 TRP 0.007 0.001 TRP I 567 HIS 0.002 0.001 HIS K 328 Details of bonding type rmsd covalent geometry : bond 0.00244 (39840) covalent geometry : angle 0.47445 (53946) hydrogen bonds : bond 0.04057 ( 1770) hydrogen bonds : angle 4.48713 ( 4920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 522 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: A 496 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7830 (mm) REVERT: B 123 GLU cc_start: 0.8178 (mp0) cc_final: 0.7881 (mp0) REVERT: B 160 ASP cc_start: 0.7927 (t70) cc_final: 0.7669 (OUTLIER) REVERT: B 255 ASP cc_start: 0.7888 (p0) cc_final: 0.7490 (p0) REVERT: B 431 MET cc_start: 0.7785 (mtp) cc_final: 0.7569 (mtp) REVERT: C 284 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.5899 (tmt) REVERT: C 441 GLU cc_start: 0.7918 (mp0) cc_final: 0.7500 (mp0) REVERT: C 496 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7484 (mp) REVERT: D 123 GLU cc_start: 0.7969 (mp0) cc_final: 0.7574 (mp0) REVERT: D 160 ASP cc_start: 0.7807 (t70) cc_final: 0.7513 (t70) REVERT: D 199 ASP cc_start: 0.8033 (m-30) cc_final: 0.7418 (p0) REVERT: E 195 MET cc_start: 0.9049 (mtp) cc_final: 0.8823 (mtm) REVERT: E 284 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.4861 (tmt) REVERT: E 496 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7368 (mp) REVERT: F 160 ASP cc_start: 0.8003 (t70) cc_final: 0.7748 (OUTLIER) REVERT: F 255 ASP cc_start: 0.7861 (p0) cc_final: 0.7644 (p0) REVERT: G 149 GLU cc_start: 0.6119 (pm20) cc_final: 0.5816 (pm20) REVERT: G 284 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.5876 (tmt) REVERT: G 441 GLU cc_start: 0.7877 (mp0) cc_final: 0.7473 (mp0) REVERT: G 496 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7447 (mp) REVERT: H 123 GLU cc_start: 0.7970 (mp0) cc_final: 0.7597 (mp0) REVERT: H 160 ASP cc_start: 0.7779 (t70) cc_final: 0.7507 (t70) REVERT: H 199 ASP cc_start: 0.8026 (m-30) cc_final: 0.7403 (p0) REVERT: H 255 ASP cc_start: 0.7814 (p0) cc_final: 0.7541 (p0) REVERT: H 302 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7844 (ttp-170) REVERT: I 195 MET cc_start: 0.9048 (mtp) cc_final: 0.8825 (mtm) REVERT: I 496 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7317 (mp) REVERT: J 160 ASP cc_start: 0.7965 (t70) cc_final: 0.7714 (t70) REVERT: J 302 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7826 (ttp-170) REVERT: K 189 GLN cc_start: 0.6708 (tp40) cc_final: 0.6407 (tp40) REVERT: K 428 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: K 496 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (mm) REVERT: L 123 GLU cc_start: 0.8152 (mp0) cc_final: 0.7885 (mp0) REVERT: L 160 ASP cc_start: 0.7870 (t70) cc_final: 0.7634 (OUTLIER) outliers start: 51 outliers final: 20 residues processed: 540 average time/residue: 0.7845 time to fit residues: 503.8547 Evaluate side-chains 530 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 502 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 573 ILE Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 428 ASP Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 235 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 77 optimal weight: 0.7980 chunk 227 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 332 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 283 ASN A 366 GLN A 504 GLN B 572 HIS C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 504 GLN F 224 ASN F 283 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 572 HIS I 152 GLN I 170 ASN I 366 GLN J 224 ASN J 366 GLN J 572 HIS K 152 GLN K 170 ASN K 283 ASN K 366 GLN K 504 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108320 restraints weight = 96406.194| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.72 r_work: 0.3163 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39840 Z= 0.100 Angle : 0.463 7.818 53946 Z= 0.239 Chirality : 0.039 0.137 6084 Planarity : 0.004 0.044 6846 Dihedral : 3.709 14.213 5274 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.39 % Allowed : 9.26 % Favored : 89.36 % 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: 1.43 (0.12), residues: 4746 helix: 2.27 (0.11), residues: 1998 sheet: -0.14 (0.18), residues: 660 loop : 0.08 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 292 TYR 0.011 0.001 TYR E 174 PHE 0.011 0.001 PHE D 452 TRP 0.007 0.001 TRP G 567 HIS 0.002 0.001 HIS I 328 Details of bonding type rmsd covalent geometry : bond 0.00224 (39840) covalent geometry : angle 0.46287 (53946) hydrogen bonds : bond 0.03856 ( 1770) hydrogen bonds : angle 4.37372 ( 4920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 522 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: A 496 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7777 (mm) REVERT: B 123 GLU cc_start: 0.7934 (mp0) cc_final: 0.7676 (mp0) REVERT: B 160 ASP cc_start: 0.7841 (t70) cc_final: 0.7602 (OUTLIER) REVERT: B 255 ASP cc_start: 0.7816 (p0) cc_final: 0.7569 (p0) REVERT: B 431 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7538 (mtp) REVERT: C 284 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.5780 (tmt) REVERT: C 290 MET cc_start: 0.8639 (mtp) cc_final: 0.8409 (mtm) REVERT: C 441 GLU cc_start: 0.7845 (mp0) cc_final: 0.7460 (mp0) REVERT: C 496 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7416 (mp) REVERT: D 160 ASP cc_start: 0.7723 (t70) cc_final: 0.7455 (t70) REVERT: D 199 ASP cc_start: 0.7849 (m-30) cc_final: 0.7301 (p0) REVERT: D 255 ASP cc_start: 0.7768 (p0) cc_final: 0.7451 (p0) REVERT: E 195 MET cc_start: 0.8911 (mtp) cc_final: 0.8645 (mtm) REVERT: E 248 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7507 (tpt-90) REVERT: E 284 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.4862 (tmt) REVERT: E 496 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7318 (mp) REVERT: F 160 ASP cc_start: 0.7965 (t70) cc_final: 0.7738 (OUTLIER) REVERT: G 149 GLU cc_start: 0.6110 (pm20) cc_final: 0.5817 (pm20) REVERT: G 284 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.5759 (tmt) REVERT: G 290 MET cc_start: 0.8648 (mtp) cc_final: 0.8393 (mtm) REVERT: G 441 GLU cc_start: 0.7824 (mp0) cc_final: 0.7445 (mp0) REVERT: G 496 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7405 (mp) REVERT: H 123 GLU cc_start: 0.7750 (mp0) cc_final: 0.7408 (mp0) REVERT: H 160 ASP cc_start: 0.7677 (t70) cc_final: 0.7456 (t70) REVERT: H 199 ASP cc_start: 0.7853 (m-30) cc_final: 0.7306 (p0) REVERT: H 255 ASP cc_start: 0.7764 (p0) cc_final: 0.7446 (p0) REVERT: I 195 MET cc_start: 0.8912 (mtp) cc_final: 0.8660 (mtm) REVERT: I 248 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7490 (tpt-90) REVERT: I 471 ASP cc_start: 0.8749 (m-30) cc_final: 0.8520 (m-30) REVERT: I 496 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7288 (mp) REVERT: J 160 ASP cc_start: 0.7935 (t70) cc_final: 0.7710 (OUTLIER) REVERT: K 189 GLN cc_start: 0.6604 (tp40) cc_final: 0.6318 (tp40) REVERT: K 496 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7800 (mm) REVERT: L 123 GLU cc_start: 0.7915 (mp0) cc_final: 0.7682 (mp0) REVERT: L 160 ASP cc_start: 0.7795 (t70) cc_final: 0.7588 (OUTLIER) REVERT: L 573 ILE cc_start: 0.7673 (mt) cc_final: 0.7269 (mt) outliers start: 60 outliers final: 25 residues processed: 540 average time/residue: 0.7896 time to fit residues: 508.0862 Evaluate side-chains 533 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 499 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 248 ARG Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 235 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 294 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 283 ASN A 366 GLN B 572 HIS C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 170 ASN E 504 GLN F 224 ASN F 366 GLN F 572 HIS G 152 GLN G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 170 ASN I 504 GLN J 224 ASN J 366 GLN J 572 HIS K 152 GLN K 170 ASN K 366 GLN L 572 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107153 restraints weight = 110946.556| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.88 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39840 Z= 0.113 Angle : 0.475 7.809 53946 Z= 0.245 Chirality : 0.039 0.134 6084 Planarity : 0.004 0.044 6846 Dihedral : 3.746 14.203 5274 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.34 % Allowed : 9.44 % Favored : 89.22 % 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: 1.43 (0.12), residues: 4746 helix: 2.30 (0.11), residues: 1986 sheet: -0.14 (0.18), residues: 660 loop : 0.07 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 292 TYR 0.012 0.001 TYR A 482 PHE 0.014 0.002 PHE B 452 TRP 0.006 0.001 TRP K 505 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00262 (39840) covalent geometry : angle 0.47491 (53946) hydrogen bonds : bond 0.03972 ( 1770) hydrogen bonds : angle 4.34110 ( 4920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 525 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: A 496 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7327 (mp) REVERT: B 123 GLU cc_start: 0.7939 (mp0) cc_final: 0.7692 (mp0) REVERT: B 255 ASP cc_start: 0.7852 (p0) cc_final: 0.7498 (p0) REVERT: B 573 ILE cc_start: 0.7749 (mt) cc_final: 0.7322 (mt) REVERT: C 284 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.5795 (tmt) REVERT: C 441 GLU cc_start: 0.7871 (mp0) cc_final: 0.7476 (mp0) REVERT: C 496 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7240 (mp) REVERT: C 547 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 160 ASP cc_start: 0.7812 (t70) cc_final: 0.7570 (t70) REVERT: D 199 ASP cc_start: 0.7877 (m-30) cc_final: 0.7330 (p0) REVERT: D 255 ASP cc_start: 0.7784 (p0) cc_final: 0.7500 (p0) REVERT: D 302 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7728 (ttp-170) REVERT: E 195 MET cc_start: 0.8930 (mtp) cc_final: 0.8675 (mtm) REVERT: E 248 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7547 (tpt-90) REVERT: E 284 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.4942 (tmt) REVERT: E 496 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7342 (mp) REVERT: F 160 ASP cc_start: 0.8012 (t70) cc_final: 0.7808 (OUTLIER) REVERT: F 255 ASP cc_start: 0.7645 (p0) cc_final: 0.7429 (p0) REVERT: G 149 GLU cc_start: 0.6062 (pm20) cc_final: 0.5791 (pm20) REVERT: G 189 GLN cc_start: 0.6709 (tp40) cc_final: 0.6484 (tp-100) REVERT: G 284 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.5776 (tmt) REVERT: G 290 MET cc_start: 0.8646 (mtp) cc_final: 0.8396 (mtm) REVERT: G 431 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6888 (mtp) REVERT: G 441 GLU cc_start: 0.7819 (mp0) cc_final: 0.7425 (mp0) REVERT: G 496 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7178 (mp) REVERT: G 547 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7979 (mm-30) REVERT: H 160 ASP cc_start: 0.7711 (t70) cc_final: 0.7472 (t70) REVERT: H 199 ASP cc_start: 0.7882 (m-30) cc_final: 0.7316 (p0) REVERT: H 255 ASP cc_start: 0.7770 (p0) cc_final: 0.7434 (p0) REVERT: I 195 MET cc_start: 0.8919 (mtp) cc_final: 0.8674 (mtm) REVERT: I 248 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7568 (tpt-90) REVERT: I 471 ASP cc_start: 0.8768 (m-30) cc_final: 0.8539 (m-30) REVERT: I 496 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7319 (mp) REVERT: J 160 ASP cc_start: 0.7998 (t70) cc_final: 0.7783 (OUTLIER) REVERT: K 189 GLN cc_start: 0.6617 (tp40) cc_final: 0.6329 (tp40) REVERT: K 496 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7342 (mp) REVERT: L 123 GLU cc_start: 0.7950 (mp0) cc_final: 0.7717 (mp0) REVERT: L 255 ASP cc_start: 0.7835 (p0) cc_final: 0.7488 (p0) REVERT: L 573 ILE cc_start: 0.7699 (mt) cc_final: 0.7301 (mt) outliers start: 58 outliers final: 27 residues processed: 546 average time/residue: 0.7939 time to fit residues: 517.1893 Evaluate side-chains 543 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 505 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 248 ARG Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain K residue 235 ASP Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 235 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 203 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 462 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN A 366 GLN B 572 HIS C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 152 GLN E 170 ASN E 366 GLN E 504 GLN F 224 ASN F 283 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 170 ASN I 366 GLN I 504 GLN J 224 ASN J 283 ASN J 366 GLN J 572 HIS K 152 GLN K 170 ASN K 366 GLN L 572 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104105 restraints weight = 98838.378| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.73 r_work: 0.3109 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39840 Z= 0.188 Angle : 0.548 8.333 53946 Z= 0.285 Chirality : 0.043 0.147 6084 Planarity : 0.005 0.051 6846 Dihedral : 4.101 14.813 5274 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.29 % Allowed : 9.83 % Favored : 88.87 % 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: 1.11 (0.12), residues: 4746 helix: 1.97 (0.11), residues: 1980 sheet: -0.41 (0.18), residues: 678 loop : 0.02 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 292 TYR 0.018 0.002 TYR A 482 PHE 0.020 0.002 PHE B 452 TRP 0.007 0.002 TRP A 410 HIS 0.006 0.001 HIS I 328 Details of bonding type rmsd covalent geometry : bond 0.00451 (39840) covalent geometry : angle 0.54822 (53946) hydrogen bonds : bond 0.04878 ( 1770) hydrogen bonds : angle 4.57972 ( 4920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7095 (tpp) REVERT: A 428 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: A 496 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 160 ASP cc_start: 0.7869 (t70) cc_final: 0.7610 (OUTLIER) REVERT: B 573 ILE cc_start: 0.7814 (mt) cc_final: 0.7405 (mt) REVERT: C 167 LYS cc_start: 0.8148 (tptm) cc_final: 0.7924 (tttt) REVERT: C 284 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.5821 (tmt) REVERT: C 431 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7081 (mtp) REVERT: C 441 GLU cc_start: 0.7879 (mp0) cc_final: 0.7465 (mp0) REVERT: C 496 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 547 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 123 GLU cc_start: 0.7808 (mp0) cc_final: 0.7593 (mp0) REVERT: D 160 ASP cc_start: 0.7921 (t70) cc_final: 0.7716 (t70) REVERT: D 199 ASP cc_start: 0.7908 (m-30) cc_final: 0.7324 (p0) REVERT: D 224 ASN cc_start: 0.7939 (t0) cc_final: 0.7672 (t160) REVERT: D 255 ASP cc_start: 0.7891 (p0) cc_final: 0.7551 (p0) REVERT: D 302 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7710 (ttp-170) REVERT: D 365 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8212 (tptt) REVERT: D 572 HIS cc_start: 0.8254 (m-70) cc_final: 0.8054 (m90) REVERT: E 195 MET cc_start: 0.9006 (mtp) cc_final: 0.8775 (mtm) REVERT: E 248 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7639 (tpt-90) REVERT: E 284 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.4911 (tmt) REVERT: E 496 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7594 (mp) REVERT: F 121 ASP cc_start: 0.8151 (m-30) cc_final: 0.7922 (m-30) REVERT: F 201 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8023 (mm-30) REVERT: G 149 GLU cc_start: 0.6187 (pm20) cc_final: 0.5933 (pm20) REVERT: G 284 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.5822 (tmt) REVERT: G 431 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: G 441 GLU cc_start: 0.7853 (mp0) cc_final: 0.7462 (mp0) REVERT: G 496 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7526 (mp) REVERT: G 547 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7963 (mm-30) REVERT: H 199 ASP cc_start: 0.7919 (m-30) cc_final: 0.7327 (p0) REVERT: H 224 ASN cc_start: 0.7905 (t0) cc_final: 0.7634 (t160) REVERT: H 255 ASP cc_start: 0.7879 (p0) cc_final: 0.7538 (p0) REVERT: H 364 ASP cc_start: 0.8651 (t70) cc_final: 0.8415 (t70) REVERT: I 195 MET cc_start: 0.9009 (mtp) cc_final: 0.8780 (mtm) REVERT: I 248 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7658 (tpt-90) REVERT: I 255 ASP cc_start: 0.7168 (t70) cc_final: 0.6954 (p0) REVERT: I 284 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.4812 (tmt) REVERT: I 471 ASP cc_start: 0.8780 (m-30) cc_final: 0.8550 (m-30) REVERT: I 496 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7575 (mp) REVERT: J 121 ASP cc_start: 0.8119 (m-30) cc_final: 0.7892 (m-30) REVERT: J 201 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8035 (mm-30) REVERT: K 189 GLN cc_start: 0.6808 (tp40) cc_final: 0.6515 (tp40) REVERT: K 366 GLN cc_start: 0.8578 (mt0) cc_final: 0.8267 (mt0) REVERT: K 496 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7623 (mp) REVERT: L 160 ASP cc_start: 0.7824 (t70) cc_final: 0.7567 (OUTLIER) outliers start: 56 outliers final: 20 residues processed: 559 average time/residue: 0.7682 time to fit residues: 513.6946 Evaluate side-chains 573 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 538 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 248 ARG Chi-restraints excluded: chain I residue 284 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 235 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 287 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 460 optimal weight: 0.6980 chunk 361 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 430 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN B 572 HIS C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 504 GLN E 170 ASN E 366 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN G 189 GLN G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 170 ASN I 366 GLN I 504 GLN J 224 ASN J 366 GLN J 572 HIS K 152 GLN K 170 ASN L 366 GLN L 572 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107571 restraints weight = 88159.589| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.61 r_work: 0.3164 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39840 Z= 0.106 Angle : 0.479 7.889 53946 Z= 0.248 Chirality : 0.039 0.183 6084 Planarity : 0.004 0.042 6846 Dihedral : 3.845 14.307 5274 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.04 % Allowed : 10.46 % Favored : 88.50 % 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: 1.33 (0.12), residues: 4746 helix: 2.18 (0.12), residues: 1998 sheet: -0.15 (0.18), residues: 648 loop : 0.02 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 292 TYR 0.011 0.001 TYR I 174 PHE 0.011 0.001 PHE E 253 TRP 0.008 0.001 TRP E 567 HIS 0.002 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00242 (39840) covalent geometry : angle 0.47884 (53946) hydrogen bonds : bond 0.03896 ( 1770) hydrogen bonds : angle 4.35572 ( 4920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 548 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7031 (tpp) REVERT: A 428 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: A 496 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 123 GLU cc_start: 0.8198 (mp0) cc_final: 0.7925 (mp0) REVERT: B 160 ASP cc_start: 0.7898 (t70) cc_final: 0.7684 (OUTLIER) REVERT: B 573 ILE cc_start: 0.7748 (mt) cc_final: 0.7341 (mt) REVERT: C 167 LYS cc_start: 0.8075 (tptm) cc_final: 0.7867 (tttt) REVERT: C 284 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.5783 (tmt) REVERT: C 431 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7023 (mtp) REVERT: C 441 GLU cc_start: 0.7965 (mp0) cc_final: 0.7545 (mp0) REVERT: C 496 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7473 (mp) REVERT: C 547 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 123 GLU cc_start: 0.8021 (mp0) cc_final: 0.7816 (mp0) REVERT: D 160 ASP cc_start: 0.8006 (t70) cc_final: 0.7805 (t70) REVERT: D 199 ASP cc_start: 0.8122 (m-30) cc_final: 0.7492 (p0) REVERT: D 201 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8586 (mm-30) REVERT: D 255 ASP cc_start: 0.7851 (p0) cc_final: 0.7551 (p0) REVERT: D 302 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7748 (ttp-170) REVERT: D 431 MET cc_start: 0.7651 (mtp) cc_final: 0.7372 (ptm) REVERT: E 195 MET cc_start: 0.8975 (mtp) cc_final: 0.8764 (mtm) REVERT: E 248 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7830 (tpt-90) REVERT: E 496 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7533 (mp) REVERT: F 121 ASP cc_start: 0.8194 (m-30) cc_final: 0.7978 (m-30) REVERT: F 255 ASP cc_start: 0.7649 (p0) cc_final: 0.7448 (p0) REVERT: G 149 GLU cc_start: 0.6202 (pm20) cc_final: 0.5989 (pm20) REVERT: G 284 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.5766 (tmt) REVERT: G 431 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7001 (mtp) REVERT: G 496 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7472 (mp) REVERT: G 547 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8181 (mm-30) REVERT: H 199 ASP cc_start: 0.8091 (m-30) cc_final: 0.7449 (p0) REVERT: H 255 ASP cc_start: 0.7837 (p0) cc_final: 0.7536 (p0) REVERT: I 195 MET cc_start: 0.8977 (mtp) cc_final: 0.8766 (mtm) REVERT: I 248 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7851 (tpt-90) REVERT: I 496 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7521 (mp) REVERT: J 121 ASP cc_start: 0.8216 (m-30) cc_final: 0.7998 (m-30) REVERT: J 167 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7598 (mmtm) REVERT: K 189 GLN cc_start: 0.6874 (tp40) cc_final: 0.6587 (tp40) REVERT: K 366 GLN cc_start: 0.8620 (mt0) cc_final: 0.8303 (mt0) REVERT: K 496 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7615 (mp) REVERT: L 123 GLU cc_start: 0.8188 (mp0) cc_final: 0.7907 (mp0) REVERT: L 160 ASP cc_start: 0.7871 (t70) cc_final: 0.7654 (OUTLIER) REVERT: L 573 ILE cc_start: 0.7748 (mt) cc_final: 0.7352 (mt) outliers start: 45 outliers final: 21 residues processed: 568 average time/residue: 0.7584 time to fit residues: 516.5979 Evaluate side-chains 558 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 525 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 573 ILE Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 248 ARG Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 475 optimal weight: 0.9990 chunk 341 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 194 optimal weight: 0.0670 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 469 optimal weight: 0.0670 chunk 3 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 chunk 343 optimal weight: 0.2980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN A 504 GLN B 197 ASN B 366 GLN B 572 HIS C 152 GLN C 170 ASN C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 170 ASN E 366 GLN E 504 GLN F 224 ASN F 366 GLN F 572 HIS G 152 GLN G 170 ASN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 152 GLN I 170 ASN I 366 GLN I 504 GLN J 224 ASN J 366 GLN J 572 HIS K 152 GLN K 170 ASN L 366 GLN L 572 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109627 restraints weight = 91476.214| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.62 r_work: 0.3196 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 39840 Z= 0.088 Angle : 0.460 9.001 53946 Z= 0.236 Chirality : 0.038 0.143 6084 Planarity : 0.004 0.046 6846 Dihedral : 3.651 14.149 5274 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.06 % Allowed : 10.85 % Favored : 88.09 % 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: 1.54 (0.12), residues: 4746 helix: 2.41 (0.12), residues: 1992 sheet: -0.14 (0.18), residues: 660 loop : 0.12 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 541 TYR 0.011 0.001 TYR D 174 PHE 0.011 0.001 PHE C 287 TRP 0.011 0.001 TRP C 567 HIS 0.002 0.001 HIS L 332 Details of bonding type rmsd covalent geometry : bond 0.00194 (39840) covalent geometry : angle 0.46031 (53946) hydrogen bonds : bond 0.03452 ( 1770) hydrogen bonds : angle 4.18127 ( 4920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 560 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 496 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 123 GLU cc_start: 0.8104 (mp0) cc_final: 0.7784 (mp0) REVERT: B 248 ARG cc_start: 0.8032 (tpp80) cc_final: 0.6859 (tpm170) REVERT: B 255 ASP cc_start: 0.7814 (p0) cc_final: 0.7460 (p0) REVERT: B 573 ILE cc_start: 0.7721 (mt) cc_final: 0.7285 (mt) REVERT: C 121 ASP cc_start: 0.8456 (m-30) cc_final: 0.8031 (t0) REVERT: C 284 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.5945 (tmt) REVERT: C 366 GLN cc_start: 0.8647 (mt0) cc_final: 0.8378 (mt0) REVERT: C 431 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6814 (mtp) REVERT: C 441 GLU cc_start: 0.7983 (mp0) cc_final: 0.7572 (mp0) REVERT: C 496 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7452 (mp) REVERT: C 541 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.7668 (mtt-85) REVERT: C 547 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8246 (mm-30) REVERT: D 167 LYS cc_start: 0.7979 (mptm) cc_final: 0.7729 (mmtm) REVERT: D 199 ASP cc_start: 0.8127 (m-30) cc_final: 0.7524 (p0) REVERT: D 201 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8557 (mm-30) REVERT: D 255 ASP cc_start: 0.7737 (p0) cc_final: 0.7414 (p0) REVERT: D 431 MET cc_start: 0.7719 (mtp) cc_final: 0.7407 (ptm) REVERT: D 498 ASN cc_start: 0.7769 (p0) cc_final: 0.7534 (p0) REVERT: E 170 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8233 (t0) REVERT: E 248 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7810 (tpt-90) REVERT: E 496 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7474 (mp) REVERT: F 201 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8060 (mm-30) REVERT: G 121 ASP cc_start: 0.8515 (m-30) cc_final: 0.8055 (t0) REVERT: G 284 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.5790 (tmt) REVERT: G 431 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7046 (mtp) REVERT: G 441 GLU cc_start: 0.7859 (mp0) cc_final: 0.7401 (mp0) REVERT: G 496 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7397 (mp) REVERT: G 541 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7674 (mtt-85) REVERT: G 547 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8184 (mm-30) REVERT: H 199 ASP cc_start: 0.8161 (m-30) cc_final: 0.7503 (p0) REVERT: H 255 ASP cc_start: 0.7732 (p0) cc_final: 0.7394 (p0) REVERT: H 498 ASN cc_start: 0.7761 (p0) cc_final: 0.7430 (p0) REVERT: H 501 GLU cc_start: 0.8340 (tt0) cc_final: 0.8129 (mt-10) REVERT: I 248 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7834 (tpt-90) REVERT: I 431 MET cc_start: 0.7562 (mmt) cc_final: 0.6920 (mtp) REVERT: I 496 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7442 (mp) REVERT: J 167 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7694 (mmtm) REVERT: J 201 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8068 (mm-30) REVERT: J 431 MET cc_start: 0.7612 (mtp) cc_final: 0.7395 (ptm) REVERT: K 189 GLN cc_start: 0.6826 (tp40) cc_final: 0.6540 (tp40) REVERT: K 496 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7482 (mp) REVERT: L 123 GLU cc_start: 0.8097 (mp0) cc_final: 0.7767 (mp0) REVERT: L 255 ASP cc_start: 0.7793 (p0) cc_final: 0.7558 (p0) REVERT: L 302 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7889 (ttp-170) REVERT: L 573 ILE cc_start: 0.7719 (mt) cc_final: 0.7293 (mt) outliers start: 46 outliers final: 22 residues processed: 579 average time/residue: 0.7538 time to fit residues: 522.9905 Evaluate side-chains 568 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 532 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 174 TYR Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 423 ASP Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 496 LEU Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 248 ARG Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 160 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 224 optimal weight: 0.8980 chunk 441 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 354 optimal weight: 0.7980 chunk 339 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 470 optimal weight: 0.8980 chunk 383 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 458 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN A 366 GLN B 366 GLN C 152 GLN C 170 ASN C 504 GLN D 366 GLN D 504 GLN D 572 HIS E 152 GLN E 170 ASN E 366 GLN E 504 GLN F 224 ASN F 366 GLN F 504 GLN F 572 HIS G 152 GLN G 170 ASN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN G 504 GLN H 366 GLN I 170 ASN I 366 GLN I 504 GLN J 224 ASN J 366 GLN J 504 GLN J 572 HIS K 152 GLN K 170 ASN K 366 GLN L 366 GLN L 572 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108860 restraints weight = 87458.258| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.71 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 39840 Z= 0.106 Angle : 0.519 32.328 53946 Z= 0.260 Chirality : 0.039 0.394 6084 Planarity : 0.004 0.120 6846 Dihedral : 3.669 14.068 5274 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.97 % Allowed : 11.38 % Favored : 87.65 % Cbeta Deviations : 0.02 % 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: 1.55 (0.12), residues: 4746 helix: 2.41 (0.12), residues: 1992 sheet: -0.10 (0.18), residues: 660 loop : 0.13 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 541 TYR 0.012 0.001 TYR E 174 PHE 0.013 0.001 PHE D 452 TRP 0.007 0.001 TRP G 567 HIS 0.002 0.001 HIS I 328 Details of bonding type rmsd covalent geometry : bond 0.00236 (39840) covalent geometry : angle 0.51891 (53946) hydrogen bonds : bond 0.03582 ( 1770) hydrogen bonds : angle 4.19022 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16604.82 seconds wall clock time: 282 minutes 19.82 seconds (16939.82 seconds total)