Starting phenix.real_space_refine on Mon Aug 25 18:50:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2025/8u7v_42012.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 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: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18456 2.51 5 N 5040 2.21 5 O 5904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "B" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "C" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "D" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "F" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "G" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "H" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 7.09, per 1000 atoms: 0.24 Number of scatterers: 29680 At special positions: 0 Unit cell: (172.84, 172.84, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 5904 8.00 N 5040 7.00 C 18456 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 40 sheets defined 42.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.929A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.146A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 452 through 470 Proline residue: A 458 - end of helix removed outlier: 3.531A pdb=" N ILE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 20 through 26 removed outlier: 4.257A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.814A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 470 Proline residue: B 458 - end of helix removed outlier: 3.551A pdb=" N ILE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'C' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.719A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 470 Proline residue: C 458 - end of helix removed outlier: 3.534A pdb=" N ILE C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'E' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 452 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'F' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.928A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 470 Proline residue: F 458 - end of helix removed outlier: 3.526A pdb=" N ILE F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'G' and resid 20 through 26 removed outlier: 4.258A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 470 Proline residue: G 458 - end of helix removed outlier: 3.600A pdb=" N ILE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'H' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 84 removed outlier: 3.721A pdb=" N ALA H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 470 Proline residue: H 458 - end of helix removed outlier: 3.534A pdb=" N ILE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.556A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.673A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.697A pdb=" N ALA C 188 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 212 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.611A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.507A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.553A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.674A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 189 removed outlier: 3.699A pdb=" N ALA H 188 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 212 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2841 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: 5.99 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4848 1.29 - 1.42: 7216 1.42 - 1.55: 17679 1.55 - 1.68: 161 1.68 - 1.81: 312 Bond restraints: 30216 Sorted by residual: bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C5 IMP C 603 " pdb=" C6 IMP C 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP B 603 " pdb=" C6 IMP B 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 30211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 40604 4.43 - 8.85: 425 8.85 - 13.28: 72 13.28 - 17.70: 11 17.70 - 22.13: 8 Bond angle restraints: 41120 Sorted by residual: angle pdb=" PA ATP A 604 " pdb=" O3A ATP A 604 " pdb=" PB ATP A 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP D 604 " pdb=" O3A ATP D 604 " pdb=" PB ATP D 604 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 124.05 12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 124.09 12.74 1.00e+00 1.00e+00 1.62e+02 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 17612 35.18 - 70.37: 631 70.37 - 105.55: 87 105.55 - 140.74: 14 140.74 - 175.92: 48 Dihedral angle restraints: 18392 sinusoidal: 7768 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' GTP B 601 " pdb=" O3A GTP B 601 " pdb=" PA GTP B 601 " pdb=" PB GTP B 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.20 175.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PA GTP G 601 " pdb=" PB GTP G 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.27 175.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP D 601 " pdb=" O3A GTP D 601 " pdb=" PA GTP D 601 " pdb=" PB GTP D 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.51 175.61 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 4664 0.203 - 0.405: 88 0.405 - 0.608: 8 0.608 - 0.810: 0 0.810 - 1.013: 16 Chirality restraints: 4776 Sorted by residual: chirality pdb=" C4' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" C5' IMP F 603 " pdb=" O4' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C4' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" C5' IMP A 603 " pdb=" O4' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C4' IMP E 603 " pdb=" C3' IMP E 603 " pdb=" C5' IMP E 603 " pdb=" O4' IMP E 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 4773 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 180 " 0.079 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 181 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 180 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR E 180 " 0.052 2.00e-02 2.50e+03 pdb=" O THR E 180 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 180 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C THR G 180 " -0.051 2.00e-02 2.50e+03 pdb=" O THR G 180 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO G 181 " 0.017 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 775 2.68 - 3.24: 30073 3.24 - 3.79: 44310 3.79 - 4.35: 62667 4.35 - 4.90: 105070 Nonbonded interactions: 242895 Sorted by model distance: nonbonded pdb=" O VAL E 73 " pdb=" OG1 THR E 74 " model vdw 2.127 3.040 nonbonded pdb=" O VAL H 73 " pdb=" OG1 THR H 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL C 73 " pdb=" OG1 THR C 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL D 73 " pdb=" OG1 THR D 74 " model vdw 2.130 3.040 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.133 3.040 ... (remaining 242890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.150 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.157 30216 Z= 0.354 Angle : 1.179 22.127 41120 Z= 0.607 Chirality : 0.089 1.013 4776 Planarity : 0.005 0.108 5056 Dihedral : 20.780 175.921 11608 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 11.98 % Favored : 87.17 % 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 aren not related in a simple way. whole: -0.95 (0.13), residues: 3704 helix: -0.08 (0.14), residues: 1376 sheet: -0.61 (0.32), residues: 216 loop : -0.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.013 0.001 TYR D 509 PHE 0.013 0.001 PHE B 456 HIS 0.003 0.001 HIS H 507 Details of bonding type rmsd covalent geometry : bond 0.00693 (30216) covalent geometry : angle 1.17914 (41120) hydrogen bonds : bond 0.14453 ( 1046) hydrogen bonds : angle 6.05735 ( 2841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 1.127 Fit side-chains REVERT: A 327 CYS cc_start: 0.8339 (p) cc_final: 0.7988 (p) REVERT: B 327 CYS cc_start: 0.8319 (p) cc_final: 0.7987 (p) REVERT: C 327 CYS cc_start: 0.8288 (p) cc_final: 0.7961 (p) REVERT: D 327 CYS cc_start: 0.8307 (p) cc_final: 0.7969 (p) REVERT: E 327 CYS cc_start: 0.8300 (p) cc_final: 0.7970 (p) REVERT: F 327 CYS cc_start: 0.8341 (p) cc_final: 0.7993 (p) REVERT: G 327 CYS cc_start: 0.8317 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8255 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.1627 time to fit residues: 103.8869 Evaluate side-chains 317 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.178785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153126 restraints weight = 38551.967| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.43 r_work: 0.3903 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30216 Z= 0.138 Angle : 0.667 7.101 41120 Z= 0.328 Chirality : 0.047 0.166 4776 Planarity : 0.005 0.052 5056 Dihedral : 19.858 155.181 5014 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.09 % Rotamer: Outliers : 1.53 % Allowed : 11.82 % Favored : 86.65 % 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 aren not related in a simple way. whole: -0.46 (0.14), residues: 3704 helix: 0.16 (0.14), residues: 1376 sheet: -0.26 (0.27), residues: 328 loop : -0.58 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 412 TYR 0.008 0.001 TYR G 509 PHE 0.011 0.001 PHE F 456 HIS 0.003 0.000 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00338 (30216) covalent geometry : angle 0.66750 (41120) hydrogen bonds : bond 0.03737 ( 1046) hydrogen bonds : angle 4.70287 ( 2841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 0.853 Fit side-chains REVERT: A 48 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: A 512 LEU cc_start: 0.5904 (tt) cc_final: 0.5697 (tp) REVERT: B 48 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: B 139 PHE cc_start: 0.4960 (t80) cc_final: 0.4723 (t80) REVERT: B 144 ILE cc_start: 0.7817 (mm) cc_final: 0.7556 (mm) REVERT: B 512 LEU cc_start: 0.5950 (tt) cc_final: 0.5734 (tp) REVERT: C 33 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8886 (m-40) REVERT: C 512 LEU cc_start: 0.5982 (tt) cc_final: 0.5746 (tp) REVERT: D 144 ILE cc_start: 0.7835 (mm) cc_final: 0.7526 (mm) REVERT: D 512 LEU cc_start: 0.5982 (tt) cc_final: 0.5772 (tp) REVERT: E 144 ILE cc_start: 0.7824 (mm) cc_final: 0.7514 (mm) REVERT: E 512 LEU cc_start: 0.5960 (tt) cc_final: 0.5736 (tp) REVERT: F 48 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: F 512 LEU cc_start: 0.5896 (tt) cc_final: 0.5678 (tp) REVERT: G 48 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: G 144 ILE cc_start: 0.7812 (mm) cc_final: 0.7543 (mm) REVERT: G 512 LEU cc_start: 0.5932 (tt) cc_final: 0.5728 (tp) REVERT: H 33 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8891 (m-40) REVERT: H 512 LEU cc_start: 0.5972 (tt) cc_final: 0.5737 (tp) outliers start: 47 outliers final: 34 residues processed: 384 average time/residue: 0.1383 time to fit residues: 93.6928 Evaluate side-chains 334 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 119 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 163 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143374 restraints weight = 38773.732| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.48 r_work: 0.3769 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30216 Z= 0.224 Angle : 0.711 7.561 41120 Z= 0.353 Chirality : 0.049 0.176 4776 Planarity : 0.005 0.045 5056 Dihedral : 19.050 157.671 5008 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 3.32 % Allowed : 14.03 % Favored : 82.65 % 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 aren not related in a simple way. whole: -0.63 (0.14), residues: 3704 helix: -0.06 (0.14), residues: 1368 sheet: -0.01 (0.33), residues: 216 loop : -0.64 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 203 TYR 0.012 0.002 TYR F 294 PHE 0.020 0.002 PHE G 139 HIS 0.005 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00563 (30216) covalent geometry : angle 0.71062 (41120) hydrogen bonds : bond 0.04521 ( 1046) hydrogen bonds : angle 4.78681 ( 2841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 331 time to evaluate : 0.859 Fit side-chains REVERT: A 135 MET cc_start: 0.8411 (tmm) cc_final: 0.7982 (tmm) REVERT: A 144 ILE cc_start: 0.8352 (mm) cc_final: 0.7984 (mt) REVERT: A 448 GLN cc_start: 0.8382 (mm110) cc_final: 0.8041 (tt0) REVERT: A 483 MET cc_start: 0.8871 (tmm) cc_final: 0.8483 (tmm) REVERT: B 135 MET cc_start: 0.8387 (tmm) cc_final: 0.7958 (tmm) REVERT: B 144 ILE cc_start: 0.8262 (mm) cc_final: 0.7917 (mm) REVERT: B 500 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5494 (mt-10) REVERT: C 117 ASP cc_start: 0.8152 (m-30) cc_final: 0.7920 (p0) REVERT: C 135 MET cc_start: 0.8367 (tmm) cc_final: 0.7928 (tmm) REVERT: C 144 ILE cc_start: 0.8266 (mm) cc_final: 0.8054 (mm) REVERT: C 500 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: D 135 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7977 (tmm) REVERT: D 483 MET cc_start: 0.8851 (tmm) cc_final: 0.8447 (tmm) REVERT: D 500 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: E 135 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7981 (tmm) REVERT: E 483 MET cc_start: 0.8849 (tmm) cc_final: 0.8441 (tmm) REVERT: E 500 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5843 (mt-10) REVERT: F 135 MET cc_start: 0.8429 (tmm) cc_final: 0.7997 (tmm) REVERT: F 144 ILE cc_start: 0.8364 (mm) cc_final: 0.7993 (mt) REVERT: F 448 GLN cc_start: 0.8366 (mm110) cc_final: 0.8041 (tt0) REVERT: F 483 MET cc_start: 0.8880 (tmm) cc_final: 0.8485 (tmm) REVERT: G 135 MET cc_start: 0.8393 (tmm) cc_final: 0.7962 (tmm) REVERT: G 500 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5497 (mt-10) REVERT: H 117 ASP cc_start: 0.8149 (m-30) cc_final: 0.7922 (p0) REVERT: H 135 MET cc_start: 0.8389 (tmm) cc_final: 0.7949 (tmm) REVERT: H 144 ILE cc_start: 0.8275 (mm) cc_final: 0.8050 (mm) REVERT: H 184 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6819 (mt-10) REVERT: H 500 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5849 (mt-10) outliers start: 102 outliers final: 54 residues processed: 411 average time/residue: 0.1499 time to fit residues: 105.9164 Evaluate side-chains 354 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 370 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 292 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN C 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153218 restraints weight = 38045.105| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.38 r_work: 0.3914 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30216 Z= 0.116 Angle : 0.584 6.361 41120 Z= 0.287 Chirality : 0.044 0.160 4776 Planarity : 0.004 0.044 5056 Dihedral : 18.034 153.725 5000 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 2.60 % Allowed : 16.21 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3704 helix: 0.36 (0.14), residues: 1376 sheet: -0.15 (0.29), residues: 280 loop : -0.39 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.008 0.001 TYR C 348 PHE 0.010 0.001 PHE F 456 HIS 0.002 0.000 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00283 (30216) covalent geometry : angle 0.58443 (41120) hydrogen bonds : bond 0.03204 ( 1046) hydrogen bonds : angle 4.35879 ( 2841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 1.181 Fit side-chains REVERT: A 33 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8994 (m-40) REVERT: A 135 MET cc_start: 0.8458 (tmm) cc_final: 0.7995 (tmm) REVERT: A 448 GLN cc_start: 0.8167 (mm110) cc_final: 0.7931 (tt0) REVERT: A 500 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5794 (mt-10) REVERT: B 135 MET cc_start: 0.8361 (tmm) cc_final: 0.7895 (tmm) REVERT: B 500 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: C 135 MET cc_start: 0.8309 (tmm) cc_final: 0.7922 (tmm) REVERT: C 144 ILE cc_start: 0.8239 (mm) cc_final: 0.8034 (mm) REVERT: C 500 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5616 (mt-10) REVERT: D 135 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7913 (tmm) REVERT: D 483 MET cc_start: 0.8852 (tmm) cc_final: 0.8644 (tmm) REVERT: D 500 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5590 (mt-10) REVERT: E 33 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8991 (m-40) REVERT: E 135 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: E 500 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5583 (mt-10) REVERT: F 135 MET cc_start: 0.8399 (tmm) cc_final: 0.7939 (tmm) REVERT: F 500 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5745 (mt-10) REVERT: G 135 MET cc_start: 0.8441 (tmm) cc_final: 0.7971 (tmm) REVERT: G 500 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5754 (mt-10) REVERT: H 135 MET cc_start: 0.8394 (tmm) cc_final: 0.7940 (tmm) REVERT: H 144 ILE cc_start: 0.8299 (mm) cc_final: 0.8083 (mm) REVERT: H 500 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5613 (mt-10) outliers start: 80 outliers final: 39 residues processed: 375 average time/residue: 0.1635 time to fit residues: 104.9299 Evaluate side-chains 337 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 201 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 265 optimal weight: 0.0170 chunk 297 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN G 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.164002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135682 restraints weight = 38018.783| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.56 r_work: 0.3668 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30216 Z= 0.119 Angle : 0.579 6.764 41120 Z= 0.282 Chirality : 0.044 0.159 4776 Planarity : 0.004 0.047 5056 Dihedral : 17.625 153.850 5000 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.94 % Favored : 95.84 % Rotamer: Outliers : 3.71 % Allowed : 15.10 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3704 helix: 0.53 (0.14), residues: 1376 sheet: -0.23 (0.28), residues: 280 loop : -0.30 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.008 0.001 TYR C 348 PHE 0.009 0.001 PHE F 456 HIS 0.001 0.000 HIS E 507 Details of bonding type rmsd covalent geometry : bond 0.00290 (30216) covalent geometry : angle 0.57892 (41120) hydrogen bonds : bond 0.03211 ( 1046) hydrogen bonds : angle 4.24231 ( 2841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 342 time to evaluate : 1.187 Fit side-chains REVERT: A 204 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 500 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: B 204 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 483 MET cc_start: 0.8984 (tmm) cc_final: 0.8650 (tmm) REVERT: B 500 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5893 (mt-10) REVERT: C 135 MET cc_start: 0.8252 (tmm) cc_final: 0.7770 (tmm) REVERT: C 144 ILE cc_start: 0.8170 (mm) cc_final: 0.7938 (mm) REVERT: C 204 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (p) REVERT: C 500 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5760 (mt-10) REVERT: D 204 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.7891 (p) REVERT: D 500 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: E 204 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7909 (p) REVERT: E 500 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5824 (mt-10) REVERT: F 204 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7914 (p) REVERT: F 500 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5846 (mt-10) REVERT: G 204 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7962 (p) REVERT: G 500 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: H 144 ILE cc_start: 0.8107 (mm) cc_final: 0.7858 (mm) REVERT: H 204 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7854 (p) REVERT: H 500 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5734 (mt-10) outliers start: 114 outliers final: 65 residues processed: 430 average time/residue: 0.1860 time to fit residues: 132.5775 Evaluate side-chains 380 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 299 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 84 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 33 ASN C 21 GLN C 33 ASN D 21 GLN D 33 ASN E 21 GLN F 21 GLN F 33 ASN G 21 GLN G 33 ASN H 21 GLN H 33 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136165 restraints weight = 37840.125| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.55 r_work: 0.3677 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30216 Z= 0.116 Angle : 0.572 7.998 41120 Z= 0.277 Chirality : 0.044 0.171 4776 Planarity : 0.004 0.044 5056 Dihedral : 17.250 154.202 5000 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 3.12 % Allowed : 15.30 % Favored : 81.58 % 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 aren not related in a simple way. whole: 0.02 (0.14), residues: 3704 helix: 0.65 (0.14), residues: 1376 sheet: -0.53 (0.26), residues: 320 loop : -0.26 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.010 0.001 TYR E 348 PHE 0.009 0.001 PHE A 456 HIS 0.001 0.000 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00277 (30216) covalent geometry : angle 0.57186 (41120) hydrogen bonds : bond 0.03079 ( 1046) hydrogen bonds : angle 4.15888 ( 2841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 330 time to evaluate : 0.805 Fit side-chains REVERT: A 500 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5858 (mt-10) REVERT: B 204 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7876 (p) REVERT: B 500 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.5887 (mt-10) REVERT: C 500 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5760 (mt-10) REVERT: D 204 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7860 (p) REVERT: D 500 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5743 (mt-10) REVERT: E 204 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 500 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: F 500 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: G 204 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7884 (p) REVERT: G 483 MET cc_start: 0.9019 (tmm) cc_final: 0.8764 (tmm) REVERT: G 500 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5866 (mt-10) REVERT: H 500 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5753 (mt-10) outliers start: 96 outliers final: 59 residues processed: 412 average time/residue: 0.1631 time to fit residues: 113.5548 Evaluate side-chains 364 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 293 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 154 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 345 optimal weight: 0.0010 chunk 65 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN C 33 ASN D 33 ASN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133293 restraints weight = 38169.561| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.59 r_work: 0.3641 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30216 Z= 0.138 Angle : 0.592 8.784 41120 Z= 0.287 Chirality : 0.045 0.162 4776 Planarity : 0.004 0.040 5056 Dihedral : 17.244 155.292 5000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 3.06 % Allowed : 15.30 % Favored : 81.64 % 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 aren not related in a simple way. whole: -0.11 (0.14), residues: 3704 helix: 0.57 (0.14), residues: 1384 sheet: -0.60 (0.26), residues: 320 loop : -0.36 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.010 0.001 TYR C 348 PHE 0.010 0.001 PHE B 35 HIS 0.002 0.000 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00340 (30216) covalent geometry : angle 0.59187 (41120) hydrogen bonds : bond 0.03296 ( 1046) hydrogen bonds : angle 4.22569 ( 2841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 310 time to evaluate : 1.170 Fit side-chains REVERT: A 204 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 500 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.5919 (mt-10) REVERT: B 204 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7893 (p) REVERT: B 500 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5974 (mt-10) REVERT: C 500 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5846 (mt-10) REVERT: D 204 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7875 (p) REVERT: D 500 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5959 (mt-10) REVERT: E 204 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7893 (p) REVERT: E 500 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5939 (mt-10) REVERT: F 82 MET cc_start: 0.8803 (tpt) cc_final: 0.8406 (tpt) REVERT: F 204 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7906 (p) REVERT: F 500 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: G 204 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7908 (p) REVERT: G 500 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5886 (mt-10) REVERT: H 500 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5909 (mt-10) outliers start: 94 outliers final: 72 residues processed: 396 average time/residue: 0.1751 time to fit residues: 117.7004 Evaluate side-chains 363 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 277 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 303 optimal weight: 3.9990 chunk 363 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 366 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN C 33 ASN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134433 restraints weight = 38163.491| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.60 r_work: 0.3653 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30216 Z= 0.120 Angle : 0.579 9.709 41120 Z= 0.280 Chirality : 0.044 0.160 4776 Planarity : 0.004 0.039 5056 Dihedral : 17.098 156.183 5000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.97 % Favored : 96.81 % Rotamer: Outliers : 3.12 % Allowed : 15.95 % Favored : 80.92 % 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 aren not related in a simple way. whole: -0.02 (0.14), residues: 3704 helix: 0.69 (0.14), residues: 1384 sheet: -0.64 (0.26), residues: 320 loop : -0.33 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 136 TYR 0.013 0.001 TYR D 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00293 (30216) covalent geometry : angle 0.57949 (41120) hydrogen bonds : bond 0.03110 ( 1046) hydrogen bonds : angle 4.16977 ( 2841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 288 time to evaluate : 1.193 Fit side-chains REVERT: A 204 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7923 (p) REVERT: A 483 MET cc_start: 0.9011 (tmm) cc_final: 0.8766 (tmm) REVERT: A 500 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5907 (mt-10) REVERT: B 204 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7874 (p) REVERT: B 483 MET cc_start: 0.9046 (tmm) cc_final: 0.8782 (tmm) REVERT: B 500 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5903 (mt-10) REVERT: C 94 ASN cc_start: 0.9426 (t0) cc_final: 0.9127 (t0) REVERT: C 204 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7902 (p) REVERT: C 500 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: D 204 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7866 (p) REVERT: D 483 MET cc_start: 0.9048 (tmm) cc_final: 0.8844 (tmm) REVERT: D 500 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: E 204 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7880 (p) REVERT: E 483 MET cc_start: 0.9031 (tmm) cc_final: 0.8780 (tmm) REVERT: E 500 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5867 (mt-10) REVERT: F 204 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7929 (p) REVERT: F 483 MET cc_start: 0.9013 (tmm) cc_final: 0.8771 (tmm) REVERT: F 500 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.5917 (mt-10) REVERT: G 204 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7886 (p) REVERT: G 500 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5872 (mt-10) REVERT: H 94 ASN cc_start: 0.9426 (t0) cc_final: 0.9142 (t0) REVERT: H 204 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (p) REVERT: H 500 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5827 (mt-10) outliers start: 96 outliers final: 78 residues processed: 376 average time/residue: 0.1736 time to fit residues: 111.8388 Evaluate side-chains 376 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 282 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 72 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN C 33 ASN D 33 ASN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132775 restraints weight = 39696.450| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.65 r_work: 0.3624 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 30216 Z= 0.147 Angle : 0.602 10.131 41120 Z= 0.292 Chirality : 0.045 0.198 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.155 157.910 5000 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.48 % Favored : 95.30 % Rotamer: Outliers : 3.22 % Allowed : 16.60 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.14), residues: 3704 helix: 0.60 (0.14), residues: 1384 sheet: -0.74 (0.25), residues: 320 loop : -0.40 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 322 TYR 0.012 0.001 TYR D 509 PHE 0.011 0.001 PHE E 35 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00365 (30216) covalent geometry : angle 0.60216 (41120) hydrogen bonds : bond 0.03346 ( 1046) hydrogen bonds : angle 4.24237 ( 2841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 293 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 204 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 483 MET cc_start: 0.9052 (tmm) cc_final: 0.8832 (tmm) REVERT: A 500 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5961 (mt-10) REVERT: B 204 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.7892 (p) REVERT: B 500 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.5944 (mt-10) REVERT: C 204 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.7919 (p) REVERT: C 483 MET cc_start: 0.9087 (tmm) cc_final: 0.8871 (tmm) REVERT: C 500 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5911 (mt-10) REVERT: D 204 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.7887 (p) REVERT: D 500 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6013 (mt-10) REVERT: E 204 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.7899 (p) REVERT: E 483 MET cc_start: 0.9053 (tmm) cc_final: 0.8829 (tmm) REVERT: E 500 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: F 204 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7899 (p) REVERT: F 483 MET cc_start: 0.9053 (tmm) cc_final: 0.8840 (tmm) REVERT: F 500 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5980 (mt-10) REVERT: G 204 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7898 (p) REVERT: G 500 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5925 (mt-10) REVERT: H 204 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7937 (p) REVERT: H 500 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5899 (mt-10) outliers start: 99 outliers final: 67 residues processed: 382 average time/residue: 0.1737 time to fit residues: 113.4311 Evaluate side-chains 362 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 279 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 58 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 226 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 278 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 448 GLN B 33 ASN C 33 ASN D 33 ASN F 448 GLN G 33 ASN H 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135663 restraints weight = 37741.355| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.59 r_work: 0.3673 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30216 Z= 0.108 Angle : 0.567 10.696 41120 Z= 0.273 Chirality : 0.043 0.157 4776 Planarity : 0.004 0.039 5056 Dihedral : 16.816 157.265 5000 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % Favored : 79.69 % 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 aren not related in a simple way. whole: 0.07 (0.14), residues: 3704 helix: 0.84 (0.14), residues: 1384 sheet: -0.65 (0.25), residues: 320 loop : -0.32 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 224 TYR 0.014 0.001 TYR D 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00257 (30216) covalent geometry : angle 0.56655 (41120) hydrogen bonds : bond 0.02911 ( 1046) hydrogen bonds : angle 4.10258 ( 2841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 94 ASN cc_start: 0.9409 (t0) cc_final: 0.9133 (t0) REVERT: A 204 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 483 MET cc_start: 0.9034 (tmm) cc_final: 0.8786 (tmm) REVERT: A 500 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: B 94 ASN cc_start: 0.9423 (t0) cc_final: 0.9161 (t0) REVERT: B 204 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 500 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5891 (mt-10) REVERT: C 94 ASN cc_start: 0.9412 (t0) cc_final: 0.9155 (t0) REVERT: C 204 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 483 MET cc_start: 0.9063 (tmm) cc_final: 0.8860 (tmm) REVERT: C 500 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5947 (mt-10) REVERT: D 94 ASN cc_start: 0.9407 (t0) cc_final: 0.9147 (t0) REVERT: D 204 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7850 (p) REVERT: D 483 MET cc_start: 0.9050 (tmm) cc_final: 0.8848 (tmm) REVERT: D 500 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: E 94 ASN cc_start: 0.9422 (t0) cc_final: 0.9166 (t0) REVERT: E 204 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7857 (p) REVERT: E 483 MET cc_start: 0.9031 (tmm) cc_final: 0.8774 (tmm) REVERT: E 500 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.5935 (mt-10) REVERT: F 63 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8553 (p) REVERT: F 94 ASN cc_start: 0.9404 (t0) cc_final: 0.9129 (t0) REVERT: F 204 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7870 (p) REVERT: F 483 MET cc_start: 0.9028 (tmm) cc_final: 0.8784 (tmm) REVERT: F 500 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: G 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9160 (t0) REVERT: G 204 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7853 (p) REVERT: G 483 MET cc_start: 0.9040 (tmm) cc_final: 0.8818 (tmm) REVERT: G 500 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: H 94 ASN cc_start: 0.9416 (t0) cc_final: 0.9143 (t0) REVERT: H 204 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7913 (p) REVERT: H 483 MET cc_start: 0.9002 (tmm) cc_final: 0.8799 (tmm) REVERT: H 500 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5927 (mt-10) outliers start: 84 outliers final: 61 residues processed: 394 average time/residue: 0.1857 time to fit residues: 122.0863 Evaluate side-chains 367 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 339 optimal weight: 3.9990 chunk 282 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 353 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 448 GLN B 33 ASN C 21 GLN D 33 ASN D 112 GLN E 112 GLN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.165114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136587 restraints weight = 37959.455| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.59 r_work: 0.3687 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30216 Z= 0.103 Angle : 0.564 11.052 41120 Z= 0.271 Chirality : 0.043 0.156 4776 Planarity : 0.004 0.038 5056 Dihedral : 16.599 157.629 5000 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.37 % Favored : 96.44 % Rotamer: Outliers : 2.93 % Allowed : 17.74 % Favored : 79.33 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3704 helix: 0.94 (0.14), residues: 1392 sheet: -0.51 (0.25), residues: 320 loop : -0.25 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 412 TYR 0.014 0.001 TYR H 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.00240 (30216) covalent geometry : angle 0.56373 (41120) hydrogen bonds : bond 0.02828 ( 1046) hydrogen bonds : angle 4.03660 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7183.62 seconds wall clock time: 123 minutes 57.42 seconds (7437.42 seconds total)