Starting phenix.real_space_refine on Tue May 27 23:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7v_42012/05_2025/8u7v_42012.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "B" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "C" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "D" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "F" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "G" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "H" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 16.61, per 1000 atoms: 0.56 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: 8.73 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.51 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: 10.16 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4848 1.29 - 1.42: 7216 1.42 - 1.55: 17679 1.55 - 1.68: 161 1.68 - 1.81: 312 Bond restraints: 30216 Sorted by residual: bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C5 IMP C 603 " pdb=" C6 IMP C 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP B 603 " pdb=" C6 IMP B 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 30211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 40604 4.43 - 8.85: 425 8.85 - 13.28: 72 13.28 - 17.70: 11 17.70 - 22.13: 8 Bond angle restraints: 41120 Sorted by residual: angle pdb=" PA ATP A 604 " pdb=" O3A ATP A 604 " pdb=" PB ATP A 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP D 604 " pdb=" O3A ATP D 604 " pdb=" PB ATP D 604 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 124.05 12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 124.09 12.74 1.00e+00 1.00e+00 1.62e+02 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 17612 35.18 - 70.37: 631 70.37 - 105.55: 87 105.55 - 140.74: 14 140.74 - 175.92: 48 Dihedral angle restraints: 18392 sinusoidal: 7768 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' GTP B 601 " pdb=" O3A GTP B 601 " pdb=" PA GTP B 601 " pdb=" PB GTP B 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.20 175.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PA GTP G 601 " pdb=" PB GTP G 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.27 175.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP D 601 " pdb=" O3A GTP D 601 " pdb=" PA GTP D 601 " pdb=" PB GTP D 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.51 175.61 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 4664 0.203 - 0.405: 88 0.405 - 0.608: 8 0.608 - 0.810: 0 0.810 - 1.013: 16 Chirality restraints: 4776 Sorted by residual: chirality pdb=" C4' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" C5' IMP F 603 " pdb=" O4' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C4' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" C5' IMP A 603 " pdb=" O4' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C4' IMP E 603 " pdb=" C3' IMP E 603 " pdb=" C5' IMP E 603 " pdb=" O4' IMP E 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 4773 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 180 " 0.079 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 181 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 180 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR E 180 " 0.052 2.00e-02 2.50e+03 pdb=" O THR E 180 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 180 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C THR G 180 " -0.051 2.00e-02 2.50e+03 pdb=" O THR G 180 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO G 181 " 0.017 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 775 2.68 - 3.24: 30073 3.24 - 3.79: 44310 3.79 - 4.35: 62667 4.35 - 4.90: 105070 Nonbonded interactions: 242895 Sorted by model distance: nonbonded pdb=" O VAL E 73 " pdb=" OG1 THR E 74 " model vdw 2.127 3.040 nonbonded pdb=" O VAL H 73 " pdb=" OG1 THR H 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL C 73 " pdb=" OG1 THR C 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL D 73 " pdb=" OG1 THR D 74 " model vdw 2.130 3.040 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.133 3.040 ... (remaining 242890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 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: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 64.040 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.157 30216 Z= 0.354 Angle : 1.179 22.127 41120 Z= 0.607 Chirality : 0.089 1.013 4776 Planarity : 0.005 0.108 5056 Dihedral : 20.780 175.921 11608 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 11.98 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS H 507 PHE 0.013 0.001 PHE B 456 TYR 0.013 0.001 TYR D 509 ARG 0.003 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.14453 ( 1046) hydrogen bonds : angle 6.05735 ( 2841) covalent geometry : bond 0.00693 (30216) covalent geometry : angle 1.17914 (41120) *********************** 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 : 3.424 Fit side-chains REVERT: A 327 CYS cc_start: 0.8339 (p) cc_final: 0.7988 (p) REVERT: B 327 CYS cc_start: 0.8319 (p) cc_final: 0.7987 (p) REVERT: C 327 CYS cc_start: 0.8288 (p) cc_final: 0.7961 (p) REVERT: D 327 CYS cc_start: 0.8307 (p) cc_final: 0.7969 (p) REVERT: E 327 CYS cc_start: 0.8300 (p) cc_final: 0.7970 (p) REVERT: F 327 CYS cc_start: 0.8341 (p) cc_final: 0.7993 (p) REVERT: G 327 CYS cc_start: 0.8317 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8255 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.3390 time to fit residues: 214.0598 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 : 2.962 ------------------------------------------------------------------------------- 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 317 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 192 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151999 restraints weight = 38392.947| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.40 r_work: 0.3885 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30216 Z= 0.143 Angle : 0.671 7.092 41120 Z= 0.330 Chirality : 0.046 0.164 4776 Planarity : 0.005 0.053 5056 Dihedral : 19.840 154.740 5014 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.64 % Favored : 96.14 % Rotamer: Outliers : 1.66 % Allowed : 11.39 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3704 helix: 0.15 (0.14), residues: 1376 sheet: -0.32 (0.27), residues: 328 loop : -0.60 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 93 PHE 0.010 0.001 PHE F 456 TYR 0.008 0.001 TYR C 32 ARG 0.004 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1046) hydrogen bonds : angle 4.72674 ( 2841) covalent geometry : bond 0.00349 (30216) covalent geometry : angle 0.67105 (41120) *********************** 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 385 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 3.094 Fit side-chains REVERT: A 48 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: A 512 LEU cc_start: 0.5755 (tt) cc_final: 0.5547 (tp) REVERT: B 48 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: B 144 ILE cc_start: 0.7891 (mm) cc_final: 0.7569 (mm) REVERT: B 512 LEU cc_start: 0.5994 (tt) cc_final: 0.5740 (tp) REVERT: C 48 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 512 LEU cc_start: 0.6016 (tt) cc_final: 0.5720 (tp) REVERT: D 48 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: D 144 ILE cc_start: 0.7876 (mm) cc_final: 0.7559 (mm) REVERT: D 512 LEU cc_start: 0.6005 (tt) cc_final: 0.5738 (tp) REVERT: E 48 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: E 144 ILE cc_start: 0.7870 (mm) cc_final: 0.7550 (mm) REVERT: E 512 LEU cc_start: 0.5985 (tt) cc_final: 0.5707 (tp) REVERT: F 48 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: F 512 LEU cc_start: 0.5942 (tt) cc_final: 0.5686 (tp) REVERT: G 48 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: G 144 ILE cc_start: 0.7884 (mm) cc_final: 0.7552 (mm) REVERT: G 512 LEU cc_start: 0.5978 (tt) cc_final: 0.5733 (tp) REVERT: H 48 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: H 512 LEU cc_start: 0.5997 (tt) cc_final: 0.5719 (tp) outliers start: 51 outliers final: 34 residues processed: 382 average time/residue: 0.3256 time to fit residues: 218.1133 Evaluate side-chains 340 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 3.186 ------------------------------------------------------------------------------- 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 278 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 292 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.168449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142088 restraints weight = 38665.636| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.43 r_work: 0.3758 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30216 Z= 0.265 Angle : 0.739 7.545 41120 Z= 0.368 Chirality : 0.051 0.178 4776 Planarity : 0.005 0.045 5056 Dihedral : 19.360 156.226 5008 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.08 % Favored : 94.71 % Rotamer: Outliers : 3.09 % Allowed : 14.03 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3704 helix: -0.22 (0.14), residues: 1376 sheet: -0.09 (0.34), residues: 216 loop : -0.70 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 372 PHE 0.017 0.002 PHE B 490 TYR 0.012 0.002 TYR H 282 ARG 0.003 0.001 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 1046) hydrogen bonds : angle 4.90265 ( 2841) covalent geometry : bond 0.00671 (30216) covalent geometry : angle 0.73939 (41120) *********************** 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 411 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 316 time to evaluate : 3.169 Fit side-chains REVERT: A 135 MET cc_start: 0.8403 (tmm) cc_final: 0.7970 (tmm) REVERT: A 448 GLN cc_start: 0.8378 (mm110) cc_final: 0.8048 (tt0) REVERT: A 483 MET cc_start: 0.8854 (tmm) cc_final: 0.8490 (tmm) REVERT: B 135 MET cc_start: 0.8383 (tmm) cc_final: 0.7958 (tmm) REVERT: B 144 ILE cc_start: 0.8261 (mm) cc_final: 0.7922 (mm) REVERT: C 117 ASP cc_start: 0.8182 (m-30) cc_final: 0.7928 (p0) REVERT: C 135 MET cc_start: 0.8379 (tmm) cc_final: 0.7926 (tmm) REVERT: C 144 ILE cc_start: 0.8291 (mm) cc_final: 0.8080 (mm) REVERT: C 184 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6762 (mt-10) REVERT: C 500 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5890 (mt-10) REVERT: D 117 ASP cc_start: 0.8174 (m-30) cc_final: 0.7944 (p0) REVERT: D 135 MET cc_start: 0.8406 (tmm) cc_final: 0.7968 (tmm) REVERT: D 144 ILE cc_start: 0.8266 (mm) cc_final: 0.7966 (mm) REVERT: D 483 MET cc_start: 0.8846 (tmm) cc_final: 0.8452 (tmm) REVERT: D 500 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5743 (mt-10) REVERT: E 117 ASP cc_start: 0.8168 (m-30) cc_final: 0.7943 (p0) REVERT: E 135 MET cc_start: 0.8408 (tmm) cc_final: 0.7971 (tmm) REVERT: E 144 ILE cc_start: 0.8260 (mm) cc_final: 0.7959 (mm) REVERT: E 483 MET cc_start: 0.8850 (tmm) cc_final: 0.8449 (tmm) REVERT: E 500 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5721 (mt-10) REVERT: F 135 MET cc_start: 0.8418 (tmm) cc_final: 0.7983 (tmm) REVERT: F 448 GLN cc_start: 0.8363 (mm110) cc_final: 0.8042 (tt0) REVERT: F 483 MET cc_start: 0.8859 (tmm) cc_final: 0.8491 (tmm) REVERT: G 135 MET cc_start: 0.8398 (tmm) cc_final: 0.7968 (tmm) REVERT: H 117 ASP cc_start: 0.8171 (m-30) cc_final: 0.7925 (p0) REVERT: H 135 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: H 144 ILE cc_start: 0.8177 (mm) cc_final: 0.7931 (mm) REVERT: H 184 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6836 (mt-10) REVERT: H 500 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5873 (mt-10) outliers start: 95 outliers final: 56 residues processed: 392 average time/residue: 0.3551 time to fit residues: 237.3484 Evaluate side-chains 350 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 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 120 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 355 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 350 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 356 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4241 r_free = 0.4241 target = 0.178408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152111 restraints weight = 38480.177| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.46 r_work: 0.3888 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30216 Z= 0.120 Angle : 0.597 6.467 41120 Z= 0.295 Chirality : 0.045 0.164 4776 Planarity : 0.004 0.048 5056 Dihedral : 18.325 153.324 5000 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.81 % Favored : 96.98 % Rotamer: Outliers : 2.73 % Allowed : 15.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3704 helix: 0.31 (0.14), residues: 1368 sheet: 0.05 (0.33), residues: 216 loop : -0.47 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 466 PHE 0.010 0.001 PHE G 139 TYR 0.009 0.001 TYR B 348 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 1046) hydrogen bonds : angle 4.46205 ( 2841) covalent geometry : bond 0.00294 (30216) covalent geometry : angle 0.59706 (41120) *********************** 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 419 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 3.469 Fit side-chains REVERT: A 135 MET cc_start: 0.8507 (tmm) cc_final: 0.8047 (tmm) REVERT: A 448 GLN cc_start: 0.8253 (mm110) cc_final: 0.7925 (tt0) REVERT: A 500 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5767 (mt-10) REVERT: B 135 MET cc_start: 0.8392 (tmm) cc_final: 0.7931 (tmm) REVERT: B 500 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5625 (mt-10) REVERT: C 135 MET cc_start: 0.8310 (tmm) cc_final: 0.7908 (tmm) REVERT: C 500 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.5779 (mt-10) REVERT: D 33 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.9018 (m-40) REVERT: D 135 MET cc_start: 0.8398 (tmm) cc_final: 0.7931 (tmm) REVERT: D 500 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5720 (mt-10) REVERT: E 135 MET cc_start: 0.8453 (tmm) cc_final: 0.7984 (tmm) REVERT: E 500 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5696 (mt-10) REVERT: F 33 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.9015 (m-40) REVERT: F 135 MET cc_start: 0.8449 (tmm) cc_final: 0.7992 (tmm) REVERT: F 448 GLN cc_start: 0.8192 (mm110) cc_final: 0.7909 (tt0) REVERT: F 500 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5765 (mt-10) REVERT: G 135 MET cc_start: 0.8463 (tmm) cc_final: 0.8003 (tmm) REVERT: G 500 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5564 (mt-10) REVERT: H 135 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7914 (tmm) REVERT: H 144 ILE cc_start: 0.8233 (mm) cc_final: 0.8018 (mm) REVERT: H 184 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6821 (mt-10) REVERT: H 500 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.5765 (mt-10) outliers start: 84 outliers final: 46 residues processed: 391 average time/residue: 0.3431 time to fit residues: 226.9096 Evaluate side-chains 354 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 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 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 82 MET 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 82 MET 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 33 ASN 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 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 361 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 332 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4073 r_free = 0.4073 target = 0.161075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132431 restraints weight = 37812.345| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.59 r_work: 0.3634 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30216 Z= 0.156 Angle : 0.619 6.505 41120 Z= 0.305 Chirality : 0.046 0.163 4776 Planarity : 0.004 0.043 5056 Dihedral : 18.037 154.578 5000 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 3.78 % Allowed : 15.10 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3704 helix: 0.30 (0.14), residues: 1368 sheet: -0.22 (0.32), residues: 216 loop : -0.46 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 507 PHE 0.012 0.002 PHE A 35 TYR 0.009 0.001 TYR E 348 ARG 0.002 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1046) hydrogen bonds : angle 4.43837 ( 2841) covalent geometry : bond 0.00386 (30216) covalent geometry : angle 0.61939 (41120) *********************** 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 450 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 334 time to evaluate : 3.116 Fit side-chains REVERT: A 82 MET cc_start: 0.8895 (tpt) cc_final: 0.8646 (tpt) REVERT: A 135 MET cc_start: 0.8444 (tmm) cc_final: 0.7941 (tmm) REVERT: A 483 MET cc_start: 0.9023 (tmm) cc_final: 0.8820 (tmm) REVERT: B 500 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5756 (mt-10) REVERT: C 500 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5869 (mt-10) REVERT: D 204 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7803 (p) REVERT: D 483 MET cc_start: 0.9026 (tmm) cc_final: 0.8783 (tmm) REVERT: D 500 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.5799 (mt-10) REVERT: E 204 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7814 (p) REVERT: E 483 MET cc_start: 0.9023 (tmm) cc_final: 0.8791 (tmm) REVERT: E 500 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5786 (mt-10) REVERT: F 82 MET cc_start: 0.8874 (tpt) cc_final: 0.8672 (tpt) REVERT: F 135 MET cc_start: 0.8448 (tmm) cc_final: 0.7946 (tmm) REVERT: F 483 MET cc_start: 0.9025 (tmm) cc_final: 0.8825 (tmm) REVERT: G 500 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5800 (mt-10) REVERT: H 500 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5860 (mt-10) outliers start: 116 outliers final: 73 residues processed: 417 average time/residue: 0.3409 time to fit residues: 243.0259 Evaluate side-chains 371 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 82 MET 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 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 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 82 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 216 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 279 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN C 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131959 restraints weight = 39587.328| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.64 r_work: 0.3606 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30216 Z= 0.162 Angle : 0.622 8.568 41120 Z= 0.306 Chirality : 0.046 0.164 4776 Planarity : 0.004 0.039 5056 Dihedral : 17.787 154.641 5000 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.16 % Favored : 96.63 % Rotamer: Outliers : 4.00 % Allowed : 15.79 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3704 helix: 0.34 (0.14), residues: 1368 sheet: -0.43 (0.32), residues: 216 loop : -0.51 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 507 PHE 0.010 0.002 PHE A 456 TYR 0.009 0.001 TYR E 348 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1046) hydrogen bonds : angle 4.45403 ( 2841) covalent geometry : bond 0.00407 (30216) covalent geometry : angle 0.62200 (41120) *********************** 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 434 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 311 time to evaluate : 3.251 Fit side-chains REVERT: A 204 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7925 (p) REVERT: A 260 LEU cc_start: 0.8724 (tt) cc_final: 0.8506 (tp) REVERT: A 483 MET cc_start: 0.9029 (tmm) cc_final: 0.8774 (tmm) REVERT: A 500 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5720 (mt-10) REVERT: B 204 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 500 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: C 260 LEU cc_start: 0.8717 (tt) cc_final: 0.8500 (tp) REVERT: C 500 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5911 (mt-10) REVERT: D 204 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.7967 (p) REVERT: D 483 MET cc_start: 0.9079 (tmm) cc_final: 0.8813 (tmm) REVERT: D 500 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5917 (mt-10) REVERT: E 82 MET cc_start: 0.8836 (tpt) cc_final: 0.8563 (tpt) REVERT: E 204 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.7977 (p) REVERT: E 483 MET cc_start: 0.9077 (tmm) cc_final: 0.8818 (tmm) REVERT: E 500 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5895 (mt-10) REVERT: F 204 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7939 (p) REVERT: F 260 LEU cc_start: 0.8722 (tt) cc_final: 0.8508 (tp) REVERT: F 483 MET cc_start: 0.9040 (tmm) cc_final: 0.8793 (tmm) REVERT: F 500 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5688 (mt-10) REVERT: G 204 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7977 (p) REVERT: G 483 MET cc_start: 0.9061 (tmm) cc_final: 0.8774 (tmm) REVERT: G 500 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5657 (mt-10) REVERT: H 82 MET cc_start: 0.8837 (tpt) cc_final: 0.8523 (tpt) REVERT: H 500 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5895 (mt-10) outliers start: 123 outliers final: 68 residues processed: 419 average time/residue: 0.3512 time to fit residues: 245.9738 Evaluate side-chains 358 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 276 time to evaluate : 3.003 ------------------------------------------------------------------------------- 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 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 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 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 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 82 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU 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 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 76 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 313 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 33 ASN B 21 GLN B 33 ASN C 21 GLN C 33 ASN D 21 GLN E 21 GLN E 33 ASN F 21 GLN G 21 GLN G 33 ASN H 21 GLN H 33 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134110 restraints weight = 38120.898| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.56 r_work: 0.3649 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30216 Z= 0.119 Angle : 0.590 7.919 41120 Z= 0.286 Chirality : 0.044 0.158 4776 Planarity : 0.004 0.041 5056 Dihedral : 17.407 155.077 5000 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.78 % Favored : 96.00 % Rotamer: Outliers : 2.80 % Allowed : 16.57 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3704 helix: 0.54 (0.15), residues: 1368 sheet: -0.70 (0.26), residues: 320 loop : -0.43 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 466 PHE 0.010 0.001 PHE F 456 TYR 0.008 0.001 TYR F 348 ARG 0.002 0.000 ARG H 224 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1046) hydrogen bonds : angle 4.29055 ( 2841) covalent geometry : bond 0.00290 (30216) covalent geometry : angle 0.59045 (41120) *********************** 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 406 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 320 time to evaluate : 3.263 Fit side-chains REVERT: A 204 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7948 (p) REVERT: A 260 LEU cc_start: 0.8648 (tt) cc_final: 0.8395 (tp) REVERT: A 483 MET cc_start: 0.9160 (tmm) cc_final: 0.8955 (tmm) REVERT: A 500 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5803 (mt-10) REVERT: B 204 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 483 MET cc_start: 0.9053 (tmm) cc_final: 0.8720 (tmm) REVERT: B 500 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: C 82 MET cc_start: 0.8839 (tpt) cc_final: 0.8603 (tpt) REVERT: C 260 LEU cc_start: 0.8643 (tt) cc_final: 0.8394 (tp) REVERT: C 483 MET cc_start: 0.9019 (tmm) cc_final: 0.8762 (tmm) REVERT: C 500 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5796 (mt-10) REVERT: D 500 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: E 500 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: F 204 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.7959 (p) REVERT: F 260 LEU cc_start: 0.8637 (tt) cc_final: 0.8388 (tp) REVERT: F 483 MET cc_start: 0.9160 (tmm) cc_final: 0.8958 (tmm) REVERT: F 500 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5792 (mt-10) REVERT: G 204 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7931 (p) REVERT: G 483 MET cc_start: 0.9048 (tmm) cc_final: 0.8808 (tmm) REVERT: G 500 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5800 (mt-10) REVERT: H 483 MET cc_start: 0.9010 (tmm) cc_final: 0.8757 (tmm) REVERT: H 500 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5774 (mt-10) outliers start: 86 outliers final: 63 residues processed: 397 average time/residue: 0.3762 time to fit residues: 247.7821 Evaluate side-chains 370 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 3.438 ------------------------------------------------------------------------------- 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 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 126 THR Chi-restraints excluded: chain C residue 157 ILE 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 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 235 LEU 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 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 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 348 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 21 GLN B 33 ASN C 33 ASN D 33 ASN D 112 GLN E 33 ASN E 112 GLN F 33 ASN G 21 GLN G 33 ASN H 33 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.162881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134376 restraints weight = 38215.742| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.60 r_work: 0.3656 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30216 Z= 0.117 Angle : 0.585 8.789 41120 Z= 0.282 Chirality : 0.044 0.160 4776 Planarity : 0.004 0.039 5056 Dihedral : 17.142 155.053 5000 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.94 % Favored : 96.84 % Rotamer: Outliers : 3.09 % Allowed : 16.21 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3704 helix: 0.62 (0.14), residues: 1368 sheet: -0.64 (0.26), residues: 320 loop : -0.36 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 466 PHE 0.009 0.001 PHE A 456 TYR 0.013 0.001 TYR D 509 ARG 0.002 0.000 ARG G 224 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 1046) hydrogen bonds : angle 4.18565 ( 2841) covalent geometry : bond 0.00282 (30216) covalent geometry : angle 0.58483 (41120) *********************** 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 411 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 316 time to evaluate : 3.057 Fit side-chains REVERT: A 483 MET cc_start: 0.9229 (tmm) cc_final: 0.9003 (tmm) REVERT: A 500 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.5915 (mt-10) REVERT: B 82 MET cc_start: 0.8815 (tpt) cc_final: 0.8481 (tpt) REVERT: B 204 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7900 (p) REVERT: B 500 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5824 (mt-10) REVERT: C 82 MET cc_start: 0.8841 (tpt) cc_final: 0.8370 (tpt) REVERT: C 204 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7900 (p) REVERT: C 483 MET cc_start: 0.9017 (tmm) cc_final: 0.8774 (tmm) REVERT: C 500 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5835 (mt-10) REVERT: D 204 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7880 (p) REVERT: D 483 MET cc_start: 0.9049 (tmm) cc_final: 0.8686 (tmm) REVERT: D 500 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5811 (mt-10) REVERT: E 204 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7898 (p) REVERT: E 483 MET cc_start: 0.9045 (tmm) cc_final: 0.8680 (tmm) REVERT: E 500 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5801 (mt-10) REVERT: F 483 MET cc_start: 0.9228 (tmm) cc_final: 0.9006 (tmm) REVERT: F 500 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5901 (mt-10) REVERT: G 204 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7898 (p) REVERT: G 500 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5809 (mt-10) REVERT: H 204 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7910 (p) REVERT: H 483 MET cc_start: 0.9010 (tmm) cc_final: 0.8770 (tmm) REVERT: H 500 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5829 (mt-10) outliers start: 95 outliers final: 67 residues processed: 397 average time/residue: 0.3636 time to fit residues: 242.2546 Evaluate side-chains 368 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 287 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 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 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 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 158 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 117 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN G 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.163102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132597 restraints weight = 39595.545| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.65 r_work: 0.3620 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 30216 Z= 0.143 Angle : 0.600 9.380 41120 Z= 0.292 Chirality : 0.045 0.162 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.182 156.130 5000 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.97 % Favored : 95.82 % Rotamer: Outliers : 3.09 % Allowed : 16.99 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3704 helix: 0.52 (0.14), residues: 1384 sheet: -0.71 (0.26), residues: 320 loop : -0.49 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 507 PHE 0.012 0.001 PHE H 35 TYR 0.013 0.001 TYR A 509 ARG 0.002 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 1046) hydrogen bonds : angle 4.25763 ( 2841) covalent geometry : bond 0.00355 (30216) covalent geometry : angle 0.59998 (41120) *********************** 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 371 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 276 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7886 (p) REVERT: A 483 MET cc_start: 0.9136 (tmm) cc_final: 0.8870 (tmm) REVERT: A 500 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: B 82 MET cc_start: 0.8878 (tpt) cc_final: 0.8376 (tpt) REVERT: B 204 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7890 (p) REVERT: B 483 MET cc_start: 0.9061 (tmm) cc_final: 0.8828 (tmm) REVERT: B 500 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: C 204 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 500 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5880 (mt-10) REVERT: D 204 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7865 (p) REVERT: D 500 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5866 (mt-10) REVERT: E 204 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 500 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5865 (mt-10) REVERT: F 204 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7886 (p) REVERT: F 483 MET cc_start: 0.9139 (tmm) cc_final: 0.8873 (tmm) REVERT: F 500 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: G 204 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7885 (p) REVERT: G 500 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5921 (mt-10) REVERT: H 204 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7925 (p) REVERT: H 500 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.5867 (mt-10) outliers start: 95 outliers final: 67 residues processed: 359 average time/residue: 0.3421 time to fit residues: 208.3786 Evaluate side-chains 356 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 273 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 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 158 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 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 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 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 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 349 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 280 optimal weight: 0.2980 chunk 281 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 33 ASN C 33 ASN F 448 GLN 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 = 0.4072 r_free = 0.4072 target = 0.161672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133646 restraints weight = 38106.026| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.54 r_work: 0.3652 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30216 Z= 0.128 Angle : 0.586 9.940 41120 Z= 0.284 Chirality : 0.044 0.162 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.052 157.199 5000 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 2.86 % Allowed : 17.38 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3704 helix: 0.66 (0.14), residues: 1384 sheet: -0.67 (0.26), residues: 320 loop : -0.46 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 507 PHE 0.010 0.001 PHE F 456 TYR 0.014 0.001 TYR C 509 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 1046) hydrogen bonds : angle 4.20907 ( 2841) covalent geometry : bond 0.00316 (30216) covalent geometry : angle 0.58626 (41120) ********************** 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 390 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 302 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 483 MET cc_start: 0.9119 (tmm) cc_final: 0.8876 (tmm) REVERT: A 500 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: B 82 MET cc_start: 0.8850 (tpt) cc_final: 0.8286 (tpt) REVERT: B 94 ASN cc_start: 0.9432 (t0) cc_final: 0.9156 (t0) REVERT: B 204 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7857 (p) REVERT: B 483 MET cc_start: 0.9054 (tmm) cc_final: 0.8804 (tmm) REVERT: B 500 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5882 (mt-10) REVERT: C 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9134 (t0) REVERT: C 204 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 500 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5919 (mt-10) REVERT: D 204 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7864 (p) REVERT: D 500 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5872 (mt-10) REVERT: E 94 ASN cc_start: 0.9427 (t0) cc_final: 0.9143 (t0) REVERT: E 204 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.7874 (p) REVERT: E 500 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5863 (mt-10) REVERT: F 204 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7855 (p) REVERT: F 483 MET cc_start: 0.9125 (tmm) cc_final: 0.8879 (tmm) REVERT: F 500 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: G 94 ASN cc_start: 0.9424 (t0) cc_final: 0.9135 (t0) REVERT: G 204 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7853 (p) REVERT: G 500 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.5859 (mt-10) REVERT: H 94 ASN cc_start: 0.9423 (t0) cc_final: 0.9132 (t0) REVERT: H 204 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7860 (p) REVERT: H 500 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5895 (mt-10) outliers start: 88 outliers final: 67 residues processed: 378 average time/residue: 0.3441 time to fit residues: 221.2697 Evaluate side-chains 373 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 290 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 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 158 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 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 158 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 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 330 optimal weight: 1.9990 chunk 347 optimal weight: 0.8980 chunk 139 optimal weight: 0.2980 chunk 218 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 163 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN C 33 ASN 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 = 0.4094 r_free = 0.4094 target = 0.163531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135069 restraints weight = 37979.744| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.60 r_work: 0.3666 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30216 Z= 0.108 Angle : 0.573 10.005 41120 Z= 0.276 Chirality : 0.043 0.156 4776 Planarity : 0.004 0.041 5056 Dihedral : 16.787 157.261 5000 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 2.83 % Allowed : 17.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3704 helix: 0.80 (0.14), residues: 1384 sheet: -0.55 (0.26), residues: 320 loop : -0.39 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 466 PHE 0.009 0.001 PHE A 456 TYR 0.015 0.001 TYR G 509 ARG 0.002 0.000 ARG H 224 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 1046) hydrogen bonds : angle 4.10989 ( 2841) covalent geometry : bond 0.00255 (30216) covalent geometry : angle 0.57279 (41120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14486.00 seconds wall clock time: 252 minutes 1.92 seconds (15121.92 seconds total)