Starting phenix.real_space_refine on Sat Aug 8 19:43:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_42012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u7v_42012/08_2026/8u7v_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 5.72, per 1000 atoms: 0.19 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: 2.42 Conformation dependent library (CDL) restraints added in 807.4 milliseconds 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: 0.85 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: 6.63 Time building geometry restraints manager: 3.08 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: 40588 4.43 - 8.85: 417 8.85 - 13.28: 88 13.28 - 17.70: 19 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: 17604 35.18 - 70.37: 639 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 - 0.197: 4651 0.197 - 0.393: 99 0.393 - 0.590: 10 0.590 - 0.786: 0 0.786 - 0.983: 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 -2.47 -1.49 -0.98 2.00e-01 2.50e+01 2.42e+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 -2.47 -1.49 -0.98 2.00e-01 2.50e+01 2.40e+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 -2.47 -1.49 -0.98 2.00e-01 2.50e+01 2.39e+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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 25.380 Find NCS groups from input model: 0.770 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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= 0.356 Angle : 1.215 22.127 41120 Z= 0.595 Chirality : 0.088 0.983 4776 Planarity : 0.005 0.108 5056 Dihedral : 20.834 175.921 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 are 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/Z covalent geometry : bond 0.00699 / 0.36 (30216) covalent geometry : angle 1.21519 / 0.60 (41120) hydrogen bonds : bond 0.14453 / 9.53 ( 1046) hydrogen bonds : angle 6.05735 / 4.23 ( 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 : 1.100 Fit side-chains REVERT: A 327 CYS cc_start: 0.8340 (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: 0.8287 (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: 0.8316 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8256 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.1574 time to fit residues: 100.8553 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 : 1.244 ------------------------------------------------------------------------------- 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... 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 = 0.4255 r_free = 0.4255 target = 0.178677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152753 restraints weight = 38348.018| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.40 r_work: 0.3893 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30216 Z= 0.138 Angle : 0.676 6.835 41120 Z= 0.329 Chirality : 0.047 0.162 4776 Planarity : 0.005 0.053 5056 Dihedral : 19.661 154.879 5014 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.09 % Rotamer: Outliers : 1.66 % Allowed : 11.36 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3704 helix: 0.18 (0.14), residues: 1376 sheet: -0.27 (0.27), residues: 328 loop : -0.57 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 412 TYR 0.007 0.001 TYR G 282 PHE 0.011 0.001 PHE F 456 HIS 0.002 0.000 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (30216) covalent geometry : angle 0.67582 / 0.33 (41120) hydrogen bonds : bond 0.03799 / 2.62 ( 1046) hydrogen bonds : angle 4.67835 / 3.32 ( 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 388 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 0.902 Fit side-chains REVERT: A 48 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: A 512 LEU cc_start: 0.5710 (tt) cc_final: 0.5504 (tp) REVERT: B 48 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: B 144 ILE cc_start: 0.7882 (mm) cc_final: 0.7598 (mm) REVERT: B 512 LEU cc_start: 0.5750 (tt) cc_final: 0.5506 (tp) REVERT: C 48 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: C 144 ILE cc_start: 0.7703 (mm) cc_final: 0.7341 (mm) REVERT: C 512 LEU cc_start: 0.5963 (tt) cc_final: 0.5660 (tp) REVERT: D 48 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: D 144 ILE cc_start: 0.7880 (mm) cc_final: 0.7555 (mm) REVERT: D 512 LEU cc_start: 0.5963 (tt) cc_final: 0.5684 (tp) REVERT: E 48 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: E 144 ILE cc_start: 0.7868 (mm) cc_final: 0.7545 (mm) REVERT: E 512 LEU cc_start: 0.5943 (tt) cc_final: 0.5654 (tp) REVERT: F 48 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: F 512 LEU cc_start: 0.5717 (tt) cc_final: 0.5478 (tp) REVERT: G 48 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: G 144 ILE cc_start: 0.7874 (mm) cc_final: 0.7583 (mm) REVERT: G 512 LEU cc_start: 0.5926 (tt) cc_final: 0.5664 (tp) REVERT: H 48 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: H 512 LEU cc_start: 0.5936 (tt) cc_final: 0.5659 (tp) outliers start: 51 outliers final: 34 residues processed: 388 average time/residue: 0.1394 time to fit residues: 95.8817 Evaluate side-chains 339 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 48 GLU 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 48 GLU 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 48 GLU 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 48 GLU 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: 4.9990 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 360 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148377 restraints weight = 38404.303| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.43 r_work: 0.3839 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30216 Z= 0.159 Angle : 0.644 7.325 41120 Z= 0.314 Chirality : 0.047 0.167 4776 Planarity : 0.004 0.049 5056 Dihedral : 18.501 155.257 5008 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 2.93 % Allowed : 13.64 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3704 helix: 0.19 (0.14), residues: 1376 sheet: -0.04 (0.30), residues: 280 loop : -0.49 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 203 TYR 0.010 0.001 TYR B 348 PHE 0.011 0.002 PHE B 139 HIS 0.006 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (30216) covalent geometry : angle 0.64357 / 0.31 (41120) hydrogen bonds : bond 0.03861 / 2.65 ( 1046) hydrogen bonds : angle 4.53399 / 3.21 ( 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 417 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 327 time to evaluate : 1.049 Fit side-chains REVERT: B 144 ILE cc_start: 0.8075 (mm) cc_final: 0.7749 (mm) REVERT: B 500 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5530 (mt-10) REVERT: C 144 ILE cc_start: 0.8198 (mm) cc_final: 0.7795 (mm) REVERT: C 500 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: D 144 ILE cc_start: 0.8138 (mm) cc_final: 0.7810 (mm) REVERT: D 500 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5676 (mt-10) REVERT: E 144 ILE cc_start: 0.8139 (mm) cc_final: 0.7810 (mm) REVERT: E 500 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5668 (mt-10) REVERT: G 144 ILE cc_start: 0.8080 (mm) cc_final: 0.7769 (mm) REVERT: G 500 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5525 (mt-10) REVERT: H 144 ILE cc_start: 0.8112 (mm) cc_final: 0.7842 (mm) REVERT: H 500 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5690 (mt-10) outliers start: 90 outliers final: 48 residues processed: 396 average time/residue: 0.1615 time to fit residues: 109.8716 Evaluate side-chains 361 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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: 5.9990 chunk 38 optimal weight: 7.9990 chunk 370 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 154 optimal weight: 0.0170 chunk 292 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153761 restraints weight = 37787.263| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.37 r_work: 0.3902 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30216 Z= 0.098 Angle : 0.565 6.627 41120 Z= 0.274 Chirality : 0.043 0.154 4776 Planarity : 0.004 0.045 5056 Dihedral : 17.501 151.633 5000 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 2.18 % Allowed : 15.04 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3704 helix: 0.59 (0.15), residues: 1376 sheet: 0.13 (0.27), residues: 328 loop : -0.29 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 412 TYR 0.007 0.001 TYR A 348 PHE 0.010 0.001 PHE F 456 HIS 0.002 0.000 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (30216) covalent geometry : angle 0.56529 / 0.27 (41120) hydrogen bonds : bond 0.02932 / 2.02 ( 1046) hydrogen bonds : angle 4.17915 / 2.97 ( 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 437 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 370 time to evaluate : 1.081 Fit side-chains REVERT: A 500 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: B 33 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8916 (m-40) REVERT: B 144 ILE cc_start: 0.8150 (mm) cc_final: 0.7776 (mm) REVERT: B 448 GLN cc_start: 0.8193 (mm110) cc_final: 0.7965 (tt0) REVERT: B 500 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5812 (mt-10) REVERT: C 144 ILE cc_start: 0.8336 (mm) cc_final: 0.7979 (mm) REVERT: C 500 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.5759 (mt-10) REVERT: D 135 MET cc_start: 0.8464 (ttm) cc_final: 0.8068 (tmm) REVERT: D 448 GLN cc_start: 0.8173 (mm110) cc_final: 0.7963 (tt0) REVERT: D 500 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5750 (mt-10) REVERT: E 135 MET cc_start: 0.8460 (ttm) cc_final: 0.8064 (tmm) REVERT: E 144 ILE cc_start: 0.8244 (mm) cc_final: 0.7918 (mm) REVERT: E 500 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5749 (mt-10) REVERT: F 500 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5898 (mt-10) REVERT: G 144 ILE cc_start: 0.8320 (mm) cc_final: 0.8020 (mm) REVERT: G 448 GLN cc_start: 0.8202 (mm110) cc_final: 0.7975 (tt0) REVERT: G 500 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: H 135 MET cc_start: 0.8433 (ttm) cc_final: 0.8040 (tmm) REVERT: H 144 ILE cc_start: 0.8023 (mm) cc_final: 0.7811 (mm) REVERT: H 500 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5758 (mt-10) outliers start: 67 outliers final: 38 residues processed: 417 average time/residue: 0.1708 time to fit residues: 117.0157 Evaluate side-chains 348 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 235 LEU 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 33 ASN 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 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 270 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 235 LEU 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 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 235 LEU 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 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 235 LEU 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 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL 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 235 LEU Chi-restraints excluded: chain H residue 270 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: 5.9990 chunk 230 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 265 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 262 optimal weight: 0.9990 chunk 331 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.177209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151070 restraints weight = 38243.250| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.39 r_work: 0.3881 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30216 Z= 0.157 Angle : 0.620 7.357 41120 Z= 0.302 Chirality : 0.046 0.162 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.481 154.725 5000 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 3.26 % Allowed : 14.91 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3704 helix: 0.43 (0.14), residues: 1376 sheet: -0.10 (0.29), residues: 280 loop : -0.34 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 341 TYR 0.010 0.001 TYR D 348 PHE 0.012 0.002 PHE D 490 HIS 0.002 0.001 HIS H 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (30216) covalent geometry : angle 0.61991 / 0.30 (41120) hydrogen bonds : bond 0.03601 / 2.47 ( 1046) hydrogen bonds : angle 4.33306 / 3.07 ( 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 415 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 315 time to evaluate : 1.060 Fit side-chains REVERT: A 135 MET cc_start: 0.8503 (ttm) cc_final: 0.8089 (tmm) REVERT: A 500 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: B 135 MET cc_start: 0.8475 (ttm) cc_final: 0.8065 (tmm) REVERT: B 500 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5900 (mt-10) REVERT: C 135 MET cc_start: 0.8217 (tmm) cc_final: 0.7720 (tmm) REVERT: C 500 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5760 (mt-10) REVERT: D 65 LEU cc_start: 0.8024 (mt) cc_final: 0.7812 (mt) REVERT: D 135 MET cc_start: 0.8501 (ttm) cc_final: 0.8046 (tmm) REVERT: D 500 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5834 (mt-10) REVERT: E 135 MET cc_start: 0.8554 (ttm) cc_final: 0.8088 (tmm) REVERT: E 500 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5826 (mt-10) REVERT: F 135 MET cc_start: 0.8441 (ttm) cc_final: 0.8021 (tmm) REVERT: F 500 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5807 (mt-10) REVERT: G 500 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5884 (mt-10) REVERT: H 135 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: H 144 ILE cc_start: 0.8260 (mm) cc_final: 0.7977 (mm) REVERT: H 500 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5775 (mt-10) outliers start: 100 outliers final: 59 residues processed: 384 average time/residue: 0.1634 time to fit residues: 108.1240 Evaluate side-chains 356 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU 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 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 131 LEU 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 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 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 131 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 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 131 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 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 131 LEU 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 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 131 LEU 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 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 135 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 84 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 188 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 ASN C 21 GLN C 33 ASN G 21 GLN G 33 ASN H 21 GLN H 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.149544 restraints weight = 38016.841| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.40 r_work: 0.3857 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30216 Z= 0.109 Angle : 0.567 6.682 41120 Z= 0.274 Chirality : 0.044 0.158 4776 Planarity : 0.004 0.042 5056 Dihedral : 17.048 153.725 5000 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.51 % Favored : 97.27 % Rotamer: Outliers : 2.51 % Allowed : 15.62 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3704 helix: 0.64 (0.15), residues: 1368 sheet: -0.39 (0.26), residues: 320 loop : -0.23 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 412 TYR 0.008 0.001 TYR F 348 PHE 0.009 0.001 PHE A 456 HIS 0.001 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (30216) covalent geometry : angle 0.56675 / 0.27 (41120) hydrogen bonds : bond 0.02941 / 2.03 ( 1046) hydrogen bonds : angle 4.15818 / 2.96 ( 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 392 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 1.097 Fit side-chains REVERT: A 500 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5869 (mt-10) REVERT: B 82 MET cc_start: 0.8681 (tpt) cc_final: 0.8287 (tpt) REVERT: B 204 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 500 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5835 (mt-10) REVERT: C 136 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6891 (ttm-80) REVERT: C 483 MET cc_start: 0.8955 (tmm) cc_final: 0.8727 (tmm) REVERT: C 500 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5818 (mt-10) REVERT: D 204 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7864 (p) REVERT: D 500 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5844 (mt-10) REVERT: E 204 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 500 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: F 500 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: G 82 MET cc_start: 0.8679 (tpt) cc_final: 0.8280 (tpt) REVERT: G 204 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7905 (p) REVERT: G 500 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5837 (mt-10) REVERT: H 144 ILE cc_start: 0.8350 (mm) cc_final: 0.8123 (mm) REVERT: H 483 MET cc_start: 0.8953 (tmm) cc_final: 0.8730 (tmm) REVERT: H 500 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5799 (mt-10) outliers start: 77 outliers final: 51 residues processed: 379 average time/residue: 0.1671 time to fit residues: 109.0947 Evaluate side-chains 354 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL 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 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 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 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 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 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 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 455 LYS 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 204 SER Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 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 235 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 154 optimal weight: 0.5980 chunk 273 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 345 optimal weight: 0.0050 chunk 65 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 372 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN B 33 ASN C 33 ASN E 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 = 0.163140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134449 restraints weight = 38211.068| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.60 r_work: 0.3660 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30216 Z= 0.131 Angle : 0.610 9.164 41120 Z= 0.291 Chirality : 0.045 0.158 4776 Planarity : 0.004 0.041 5056 Dihedral : 16.924 154.464 5000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.37 % Favored : 95.41 % Rotamer: Outliers : 2.86 % Allowed : 15.36 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3704 helix: 0.58 (0.14), residues: 1376 sheet: -0.52 (0.26), residues: 320 loop : -0.32 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 224 TYR 0.011 0.001 TYR E 348 PHE 0.011 0.001 PHE E 35 HIS 0.002 0.001 HIS G 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (30216) covalent geometry : angle 0.61014 / 0.29 (41120) hydrogen bonds : bond 0.03310 / 2.28 ( 1046) hydrogen bonds : angle 4.19520 / 2.98 ( 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 386 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 298 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 204 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7928 (p) REVERT: A 352 GLU cc_start: 0.8521 (pp20) cc_final: 0.7673 (tp30) REVERT: A 500 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5986 (mt-10) REVERT: B 204 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7925 (p) REVERT: B 352 GLU cc_start: 0.8522 (pp20) cc_final: 0.7668 (tp30) REVERT: B 500 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.5975 (mt-10) REVERT: C 204 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 352 GLU cc_start: 0.8497 (pp20) cc_final: 0.7666 (tp30) REVERT: C 500 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5957 (mt-10) REVERT: D 204 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7927 (p) REVERT: D 352 GLU cc_start: 0.8499 (pp20) cc_final: 0.7666 (tp30) REVERT: D 500 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5966 (mt-10) REVERT: E 204 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.7953 (p) REVERT: E 352 GLU cc_start: 0.8512 (pp20) cc_final: 0.7675 (tp30) REVERT: E 500 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5966 (mt-10) REVERT: F 500 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5944 (mt-10) REVERT: G 204 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7935 (p) REVERT: G 352 GLU cc_start: 0.8532 (pp20) cc_final: 0.7678 (tp30) REVERT: G 500 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.5984 (mt-10) REVERT: H 204 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7962 (p) REVERT: H 352 GLU cc_start: 0.8499 (pp20) cc_final: 0.7666 (tp30) REVERT: H 500 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5935 (mt-10) outliers start: 88 outliers final: 56 residues processed: 378 average time/residue: 0.1637 time to fit residues: 106.8568 Evaluate side-chains 344 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE 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 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 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 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 477 ASP Chi-restraints excluded: chain C residue 500 GLU 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 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 157 ILE 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 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 384 VAL 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 204 SER Chi-restraints excluded: chain H residue 235 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 303 optimal weight: 5.9990 chunk 363 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 344 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 ASN C 33 ASN E 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132898 restraints weight = 38343.646| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.60 r_work: 0.3636 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30216 Z= 0.155 Angle : 0.629 9.132 41120 Z= 0.300 Chirality : 0.046 0.181 4776 Planarity : 0.004 0.040 5056 Dihedral : 16.991 155.900 5000 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 2.99 % Allowed : 15.69 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3704 helix: 0.52 (0.14), residues: 1384 sheet: -0.62 (0.26), residues: 320 loop : -0.44 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.012 0.001 TYR D 509 PHE 0.010 0.001 PHE F 35 HIS 0.002 0.001 HIS C 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 (30216) covalent geometry : angle 0.62921 / 0.30 (41120) hydrogen bonds : bond 0.03366 / 2.33 ( 1046) hydrogen bonds : angle 4.25786 / 3.02 ( 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 394 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 302 time to evaluate : 1.206 Fit side-chains REVERT: A 204 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 483 MET cc_start: 0.8943 (tmm) cc_final: 0.8720 (tmm) REVERT: A 500 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.5973 (mt-10) REVERT: B 204 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7917 (p) REVERT: B 500 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5967 (mt-10) REVERT: C 94 ASN cc_start: 0.9423 (t0) cc_final: 0.9155 (t0) REVERT: C 204 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.7967 (p) REVERT: C 500 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5861 (mt-10) REVERT: D 204 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.7906 (p) REVERT: D 483 MET cc_start: 0.8934 (tmm) cc_final: 0.8714 (tmm) REVERT: D 500 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: E 204 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7930 (p) REVERT: E 483 MET cc_start: 0.9011 (tmm) cc_final: 0.8795 (tmm) REVERT: E 500 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5830 (mt-10) REVERT: F 204 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7888 (p) REVERT: F 352 GLU cc_start: 0.7928 (tp30) cc_final: 0.7651 (tp30) REVERT: F 500 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: G 94 ASN cc_start: 0.9427 (t0) cc_final: 0.9159 (t0) REVERT: G 204 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7885 (p) REVERT: G 500 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.5984 (mt-10) REVERT: H 94 ASN cc_start: 0.9433 (t0) cc_final: 0.9152 (t0) REVERT: H 204 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.7975 (p) REVERT: H 500 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5854 (mt-10) outliers start: 92 outliers final: 61 residues processed: 386 average time/residue: 0.1648 time to fit residues: 109.2313 Evaluate side-chains 360 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 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 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 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 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 455 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 72 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 GLN B 33 ASN C 33 ASN E 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 = 0.4092 r_free = 0.4092 target = 0.163366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134832 restraints weight = 38138.970| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.60 r_work: 0.3663 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30216 Z= 0.122 Angle : 0.606 10.345 41120 Z= 0.287 Chirality : 0.044 0.167 4776 Planarity : 0.004 0.041 5056 Dihedral : 16.769 156.722 5000 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 2.60 % Allowed : 16.83 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3704 helix: 0.66 (0.14), residues: 1384 sheet: -0.51 (0.26), residues: 320 loop : -0.41 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 224 TYR 0.014 0.001 TYR E 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (30216) covalent geometry : angle 0.60642 / 0.29 (41120) hydrogen bonds : bond 0.03083 / 2.13 ( 1046) hydrogen bonds : angle 4.16983 / 2.97 ( 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 376 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8933 (tmm) cc_final: 0.8703 (tmm) REVERT: A 500 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.5969 (mt-10) REVERT: B 94 ASN cc_start: 0.9426 (t0) cc_final: 0.9166 (t0) REVERT: B 204 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 500 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5964 (mt-10) REVERT: C 94 ASN cc_start: 0.9412 (t0) cc_final: 0.9149 (t0) REVERT: C 204 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7952 (p) REVERT: C 500 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6009 (mt-10) REVERT: D 204 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7848 (p) REVERT: D 483 MET cc_start: 0.9015 (tmm) cc_final: 0.8777 (tmm) REVERT: D 500 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5994 (mt-10) REVERT: E 94 ASN cc_start: 0.9432 (t0) cc_final: 0.9173 (t0) REVERT: E 204 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7869 (p) REVERT: E 483 MET cc_start: 0.9004 (tmm) cc_final: 0.8777 (tmm) REVERT: E 500 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: F 204 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.7880 (p) REVERT: F 500 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5968 (mt-10) REVERT: G 94 ASN cc_start: 0.9424 (t0) cc_final: 0.9160 (t0) REVERT: G 204 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7862 (p) REVERT: G 500 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6035 (mt-10) REVERT: H 94 ASN cc_start: 0.9416 (t0) cc_final: 0.9155 (t0) REVERT: H 204 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7960 (p) REVERT: H 500 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6015 (mt-10) outliers start: 80 outliers final: 60 residues processed: 370 average time/residue: 0.1610 time to fit residues: 100.9024 Evaluate side-chains 352 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 455 LYS 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 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: 2.9990 chunk 256 optimal weight: 0.6980 chunk 45 optimal weight: 0.0030 chunk 287 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 0.0020 chunk 278 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 368 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 GLN B 21 GLN B 33 ASN C 33 ASN E 33 ASN F 21 GLN F 448 GLN G 33 ASN H 33 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137897 restraints weight = 38031.873| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.56 r_work: 0.3708 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30216 Z= 0.101 Angle : 0.589 10.906 41120 Z= 0.275 Chirality : 0.043 0.157 4776 Planarity : 0.004 0.044 5056 Dihedral : 16.385 156.237 5000 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.79 % Rotamer: Outliers : 2.25 % Allowed : 17.51 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3704 helix: 0.89 (0.14), residues: 1376 sheet: -0.34 (0.26), residues: 320 loop : -0.28 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 412 TYR 0.014 0.001 TYR D 509 PHE 0.009 0.001 PHE A 456 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (30216) covalent geometry : angle 0.58885 / 0.28 (41120) hydrogen bonds : bond 0.02797 / 1.92 ( 1046) hydrogen bonds : angle 4.00999 / 2.86 ( 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 404 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.9388 (t0) cc_final: 0.9130 (t0) REVERT: A 204 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7797 (p) REVERT: A 483 MET cc_start: 0.8936 (tmm) cc_final: 0.8661 (tmm) REVERT: A 500 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: B 94 ASN cc_start: 0.9420 (t0) cc_final: 0.9164 (t0) REVERT: B 204 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7837 (p) REVERT: B 500 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: C 94 ASN cc_start: 0.9408 (t0) cc_final: 0.9156 (t0) REVERT: C 204 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 500 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5873 (mt-10) REVERT: D 94 ASN cc_start: 0.9397 (t0) cc_final: 0.9139 (t0) REVERT: D 204 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7810 (p) REVERT: D 483 MET cc_start: 0.9016 (tmm) cc_final: 0.8735 (tmm) REVERT: D 500 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5820 (mt-10) REVERT: E 94 ASN cc_start: 0.9420 (t0) cc_final: 0.9173 (t0) REVERT: E 204 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.7824 (p) REVERT: E 483 MET cc_start: 0.9002 (tmm) cc_final: 0.8751 (tmm) REVERT: E 500 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: F 94 ASN cc_start: 0.9394 (t0) cc_final: 0.9137 (t0) REVERT: F 204 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7801 (p) REVERT: F 500 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5781 (mt-10) REVERT: G 94 ASN cc_start: 0.9416 (t0) cc_final: 0.9156 (t0) REVERT: G 204 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7828 (p) REVERT: G 500 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5946 (mt-10) REVERT: H 94 ASN cc_start: 0.9410 (t0) cc_final: 0.9155 (t0) REVERT: H 204 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7895 (p) REVERT: H 500 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5864 (mt-10) outliers start: 69 outliers final: 52 residues processed: 395 average time/residue: 0.1713 time to fit residues: 112.9924 Evaluate side-chains 360 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 270 VAL Chi-restraints excluded: chain A residue 299 VAL 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 158 VAL 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 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE 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 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 63 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 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 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 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 235 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 160 optimal weight: 0.2980 chunk 339 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 353 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 448 GLN B 33 ASN C 21 GLN C 33 ASN D 21 GLN E 21 GLN E 33 ASN G 33 ASN H 21 GLN H 33 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138125 restraints weight = 38183.880| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.58 r_work: 0.3712 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30216 Z= 0.100 Angle : 0.589 10.766 41120 Z= 0.276 Chirality : 0.043 0.157 4776 Planarity : 0.004 0.045 5056 Dihedral : 16.202 156.150 5000 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 2.47 % Allowed : 18.29 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3704 helix: 1.01 (0.14), residues: 1376 sheet: -0.25 (0.27), residues: 320 loop : -0.23 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 412 TYR 0.015 0.001 TYR A 509 PHE 0.012 0.001 PHE D 139 HIS 0.002 0.000 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (30216) covalent geometry : angle 0.58917 / 0.28 (41120) hydrogen bonds : bond 0.02763 / 1.91 ( 1046) hydrogen bonds : angle 3.97479 / 2.84 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6908.39 seconds wall clock time: 119 minutes 19.51 seconds (7159.51 seconds total)