Starting phenix.real_space_refine on Tue Oct 27 23:24:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wv9_66285/10_2026/9wv9_66285.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 24 5.49 5 Mg 16 5.21 5 S 128 5.16 5 C 16400 2.51 5 N 4408 2.21 5 O 5028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "B" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 388} Chain breaks: 1 Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "E" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3183 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 389} Chain breaks: 1 Chain: "G" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "H" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' FE': 1, ' MG': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4252 SG CYS B 127 91.659 50.695 12.371 1.00 30.37 S ATOM 10656 SG CYS D 127 40.012 82.684 12.372 1.00 30.28 S ATOM 17068 SG CYS F 127 91.642 82.687 81.681 1.00 31.21 S ATOM 23526 SG CYS H 127 40.030 50.693 81.679 1.00 31.66 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb="FE FE A1004 " occ=0.95 residue: pdb="FE FE B1004 " occ=0.83 residue: pdb="FE FE C1004 " occ=0.94 residue: pdb="FE FE D1004 " occ=0.88 residue: pdb="FE FE E1004 " occ=0.89 residue: pdb="FE FE F1004 " occ=0.83 residue: pdb="FE FE G1004 " occ=0.96 residue: pdb="FE FE H1004 " occ=0.84 Time building chain proxies: 5.72, per 1000 atoms: 0.22 Number of scatterers: 26012 At special positions: 0 Unit cell: (132.525, 135.09, 94.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 128 16.00 P 24 15.00 Mg 16 11.99 O 5028 8.00 N 4408 7.00 C 16400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 8 sheets defined 71.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.793A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.932A pdb=" N SER A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 90 Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.834A pdb=" N GLU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.534A pdb=" N GLU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 200 through 218 removed outlier: 3.586A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.775A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.677A pdb=" N VAL A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 removed outlier: 3.510A pdb=" N LEU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.634A pdb=" N ALA A 309 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.641A pdb=" N ASN A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.799A pdb=" N ILE A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.587A pdb=" N ASP A 397 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 398 " --> pdb=" O SER A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 398' Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.556A pdb=" N ILE B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 removed outlier: 3.691A pdb=" N GLU B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.997A pdb=" N TYR B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 71 through 90 Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.694A pdb=" N GLU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 125 through 128 removed outlier: 4.020A pdb=" N GLY B 128 " --> pdb=" O LEU B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 128' Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 200 through 225 removed outlier: 3.800A pdb=" N ASP B 218 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 270 through 292 removed outlier: 3.878A pdb=" N ASP B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.765A pdb=" N LEU B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 345 removed outlier: 3.506A pdb=" N GLN B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 3.770A pdb=" N ILE B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.793A pdb=" N ASP C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 71 through 90 Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.834A pdb=" N GLU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.534A pdb=" N GLU C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 200 through 218 removed outlier: 3.581A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 229 through 240 removed outlier: 3.780A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 246 through 262 removed outlier: 3.675A pdb=" N VAL C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 292 removed outlier: 3.511A pdb=" N LEU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 292 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.631A pdb=" N ALA C 309 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 345 Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.641A pdb=" N ASN C 353 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.799A pdb=" N ILE C 363 " --> pdb=" O GLU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 379 through 392 Processing helix chain 'C' and resid 394 through 398 removed outlier: 3.587A pdb=" N ASP C 397 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 398' Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.995A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 71 through 90 Processing helix chain 'D' and resid 95 through 105 removed outlier: 3.673A pdb=" N GLU D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 125 through 128 removed outlier: 4.018A pdb=" N GLY D 128 " --> pdb=" O LEU D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 200 through 225 removed outlier: 3.807A pdb=" N ASP D 218 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 270 through 292 removed outlier: 3.880A pdb=" N ASP D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 removed outlier: 3.766A pdb=" N LEU D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.507A pdb=" N GLN D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 363 removed outlier: 3.735A pdb=" N ILE D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 379 through 392 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 37 through 47 removed outlier: 3.797A pdb=" N ASP E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.857A pdb=" N SER E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 90 Processing helix chain 'E' and resid 95 through 105 removed outlier: 3.830A pdb=" N GLU E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.531A pdb=" N GLU E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 118 " --> pdb=" O HIS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 200 through 218 removed outlier: 3.578A pdb=" N ALA E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 229 through 240 removed outlier: 3.775A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'E' and resid 246 through 262 removed outlier: 3.677A pdb=" N VAL E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 292 removed outlier: 3.512A pdb=" N LEU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 292 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 323 removed outlier: 3.635A pdb=" N ALA E 309 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 345 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.643A pdb=" N ASN E 353 " --> pdb=" O ASN E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 363 removed outlier: 3.798A pdb=" N ILE E 363 " --> pdb=" O GLU E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'E' and resid 379 through 392 Processing helix chain 'E' and resid 394 through 398 removed outlier: 3.581A pdb=" N ASP E 397 " --> pdb=" O GLY E 394 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 398 " --> pdb=" O SER E 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 394 through 398' Processing helix chain 'F' and resid 3 through 17 removed outlier: 3.592A pdb=" N ILE F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 21 removed outlier: 3.627A pdb=" N GLU F 21 " --> pdb=" O SER F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 21' Processing helix chain 'F' and resid 38 through 47 removed outlier: 3.971A pdb=" N TYR F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 43 " --> pdb=" O MET F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 71 through 90 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.692A pdb=" N GLU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 125 through 128 removed outlier: 4.013A pdb=" N GLY F 128 " --> pdb=" O LEU F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 128' Processing helix chain 'F' and resid 131 through 142 Processing helix chain 'F' and resid 156 through 163 Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 200 through 225 removed outlier: 3.803A pdb=" N ASP F 218 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 240 Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 270 through 292 removed outlier: 3.882A pdb=" N ASP F 292 " --> pdb=" O ILE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 322 removed outlier: 3.783A pdb=" N LEU F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 345 removed outlier: 3.506A pdb=" N GLN F 327 " --> pdb=" O LYS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 363 removed outlier: 3.771A pdb=" N ILE F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 Processing helix chain 'F' and resid 379 through 392 Processing helix chain 'F' and resid 394 through 398 Processing helix chain 'G' and resid 3 through 18 Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 37 through 47 removed outlier: 3.799A pdb=" N ASP G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.858A pdb=" N SER G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 90 Processing helix chain 'G' and resid 95 through 105 removed outlier: 3.821A pdb=" N GLU G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.532A pdb=" N GLU G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL G 118 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 142 Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 179 through 194 Processing helix chain 'G' and resid 200 through 218 removed outlier: 3.574A pdb=" N ALA G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 225 Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.775A pdb=" N GLU G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 246 through 262 removed outlier: 3.647A pdb=" N VAL G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 292 removed outlier: 3.501A pdb=" N ILE G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 292 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 323 removed outlier: 3.646A pdb=" N ALA G 309 " --> pdb=" O HIS G 305 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 317 " --> pdb=" O LYS G 313 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 345 Processing helix chain 'G' and resid 350 through 354 removed outlier: 3.640A pdb=" N ASN G 353 " --> pdb=" O ASN G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 363 removed outlier: 3.799A pdb=" N ILE G 363 " --> pdb=" O GLU G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 379 through 392 Processing helix chain 'G' and resid 394 through 398 removed outlier: 3.582A pdb=" N ASP G 397 " --> pdb=" O GLY G 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS G 398 " --> pdb=" O SER G 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 394 through 398' Processing helix chain 'H' and resid 3 through 18 removed outlier: 3.554A pdb=" N ILE H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 21 No H-bonds generated for 'chain 'H' and resid 19 through 21' Processing helix chain 'H' and resid 38 through 47 removed outlier: 3.976A pdb=" N TYR H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA H 43 " --> pdb=" O MET H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 63 through 68 removed outlier: 3.849A pdb=" N LYS H 67 " --> pdb=" O VAL H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 90 Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.673A pdb=" N GLU H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 125 through 128 removed outlier: 4.014A pdb=" N GLY H 128 " --> pdb=" O LEU H 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 125 through 128' Processing helix chain 'H' and resid 131 through 142 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 179 through 194 Processing helix chain 'H' and resid 200 through 225 removed outlier: 3.799A pdb=" N ASP H 218 " --> pdb=" O TYR H 214 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 240 Processing helix chain 'H' and resid 243 through 245 No H-bonds generated for 'chain 'H' and resid 243 through 245' Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 270 through 292 removed outlier: 3.877A pdb=" N ASP H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 322 removed outlier: 3.767A pdb=" N LEU H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 345 removed outlier: 3.507A pdb=" N GLN H 327 " --> pdb=" O LYS H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 363 removed outlier: 3.770A pdb=" N ILE H 363 " --> pdb=" O GLU H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 379 through 392 Processing helix chain 'H' and resid 394 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA2, first strand: chain 'B' and resid 293 through 296 Processing sheet with id=AA3, first strand: chain 'C' and resid 293 through 296 Processing sheet with id=AA4, first strand: chain 'D' and resid 293 through 296 Processing sheet with id=AA5, first strand: chain 'E' and resid 293 through 296 Processing sheet with id=AA6, first strand: chain 'F' and resid 293 through 296 Processing sheet with id=AA7, first strand: chain 'G' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'H' and resid 293 through 296 1466 hydrogen bonds defined for protein. 4338 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: 4.18 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4394 1.31 - 1.43: 6939 1.43 - 1.56: 14851 1.56 - 1.69: 40 1.69 - 1.81: 224 Bond restraints: 26448 Sorted by residual: bond pdb=" C GLU C 78 " pdb=" O GLU C 78 " ideal model delta sigma weight residual 1.237 1.182 0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" C GLU E 78 " pdb=" O GLU E 78 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.19e-02 7.06e+03 1.90e+01 bond pdb=" C GLU A 78 " pdb=" O GLU A 78 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.19e-02 7.06e+03 1.90e+01 bond pdb=" C GLU G 78 " pdb=" O GLU G 78 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.19e-02 7.06e+03 1.84e+01 bond pdb=" C GLU A 78 " pdb=" N VAL A 79 " ideal model delta sigma weight residual 1.335 1.281 0.054 1.26e-02 6.30e+03 1.83e+01 ... (remaining 26443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 34931 1.44 - 2.88: 552 2.88 - 4.32: 103 4.32 - 5.75: 29 5.75 - 7.19: 10 Bond angle restraints: 35625 Sorted by residual: angle pdb=" C GLU G 78 " pdb=" CA GLU G 78 " pdb=" CB GLU G 78 " ideal model delta sigma weight residual 110.85 105.10 5.75 1.70e+00 3.46e-01 1.14e+01 angle pdb=" C GLU E 78 " pdb=" CA GLU E 78 " pdb=" CB GLU E 78 " ideal model delta sigma weight residual 110.85 105.31 5.54 1.70e+00 3.46e-01 1.06e+01 angle pdb=" C GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " ideal model delta sigma weight residual 110.85 105.37 5.48 1.70e+00 3.46e-01 1.04e+01 angle pdb=" C GLU C 78 " pdb=" CA GLU C 78 " pdb=" CB GLU C 78 " ideal model delta sigma weight residual 110.85 105.39 5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N VAL D 63 " pdb=" CA VAL D 63 " pdb=" C VAL D 63 " ideal model delta sigma weight residual 112.17 109.49 2.68 9.50e-01 1.11e+00 7.98e+00 ... (remaining 35620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 15265 32.39 - 64.77: 715 64.77 - 97.16: 61 97.16 - 129.54: 4 129.54 - 161.93: 12 Dihedral angle restraints: 16057 sinusoidal: 6618 harmonic: 9439 Sorted by residual: dihedral pdb=" O3B GTP A1002 " pdb=" O3A GTP A1002 " pdb=" PB GTP A1002 " pdb=" PA GTP A1002 " ideal model delta sinusoidal sigma weight residual -68.92 93.01 -161.93 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O3B GTP C1002 " pdb=" O3A GTP C1002 " pdb=" PB GTP C1002 " pdb=" PA GTP C1002 " ideal model delta sinusoidal sigma weight residual -68.92 90.42 -159.34 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O3B GTP E1002 " pdb=" O3A GTP E1002 " pdb=" PB GTP E1002 " pdb=" PA GTP E1002 " ideal model delta sinusoidal sigma weight residual -68.92 90.38 -159.30 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 16054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2277 0.025 - 0.049: 892 0.049 - 0.074: 514 0.074 - 0.098: 138 0.098 - 0.123: 52 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA PHE G 112 " pdb=" N PHE G 112 " pdb=" C PHE G 112 " pdb=" CB PHE G 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA PHE E 112 " pdb=" N PHE E 112 " pdb=" C PHE E 112 " pdb=" CB PHE E 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA PHE C 112 " pdb=" N PHE C 112 " pdb=" C PHE C 112 " pdb=" CB PHE C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 3870 not shown) Planarity restraints: 4532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 21 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C GLU D 21 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU D 21 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR D 22 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 21 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C GLU H 21 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU H 21 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR H 22 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 21 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C GLU B 21 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 21 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR B 22 " -0.009 2.00e-02 2.50e+03 ... (remaining 4529 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 552 2.69 - 3.25: 25319 3.25 - 3.80: 40553 3.80 - 4.35: 55089 4.35 - 4.90: 91060 Nonbonded interactions: 212573 Sorted by model distance: nonbonded pdb=" N LEU B 60 " pdb="MG MG B1001 " model vdw 2.143 2.250 nonbonded pdb=" N LEU H 60 " pdb="MG MG H1001 " model vdw 2.146 2.250 nonbonded pdb=" N LEU D 60 " pdb="MG MG D1001 " model vdw 2.151 2.250 nonbonded pdb=" N LEU F 60 " pdb="MG MG F1001 " model vdw 2.156 2.250 nonbonded pdb=" O ASN F 15 " pdb=" OG SER F 18 " model vdw 2.249 3.040 ... (remaining 212568 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 62 or resid 70 through 1004)) selection = (chain 'B' and (resid 1 through 62 or resid 70 through 1004)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 62 or resid 70 through 1004)) selection = (chain 'E' and (resid 1 through 62 or resid 70 through 1004)) selection = (chain 'F' and (resid 1 through 62 or resid 70 through 1004)) selection = (chain 'G' and (resid 1 through 62 or resid 70 through 1004)) selection = (chain 'H' and (resid 1 through 62 or resid 70 through 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.83 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.350 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.002 0.054 26448 Z= 0.138 Angle : 0.497 7.192 35625 Z= 0.264 Chirality : 0.036 0.123 3873 Planarity : 0.003 0.030 4532 Dihedral : 18.359 161.927 10019 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.15 % Allowed : 22.01 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3183 helix: 1.39 (0.11), residues: 2121 sheet: None (None), residues: 0 loop : -0.87 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 369 TYR 0.012 0.001 TYR C 214 PHE 0.027 0.001 PHE B 185 HIS 0.008 0.001 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (26448) covalent geometry : angle 0.49672 / 0.26 (35625) hydrogen bonds : bond 0.13835 / 9.20 ( 1466) hydrogen bonds : angle 4.82218 / 3.52 ( 4338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 422 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.4654 (mmp) cc_final: 0.4402 (mmm) outliers start: 4 outliers final: 12 residues processed: 422 average time/residue: 0.5758 time to fit residues: 285.4207 Evaluate side-chains 378 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 7 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 217 HIS C 217 HIS E 81 GLN E 217 HIS G 217 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150038 restraints weight = 33458.070| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.72 r_work: 0.3758 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 26448 Z= 0.167 Angle : 0.558 7.184 35625 Z= 0.290 Chirality : 0.038 0.125 3873 Planarity : 0.003 0.030 4532 Dihedral : 11.320 161.393 3712 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.06 % Allowed : 22.30 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3183 helix: 1.51 (0.11), residues: 2137 sheet: None (None), residues: 0 loop : -1.01 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 70 TYR 0.015 0.001 TYR C 214 PHE 0.025 0.002 PHE G 225 HIS 0.005 0.001 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (26448) covalent geometry : angle 0.55770 / 0.29 (35625) hydrogen bonds : bond 0.05654 / 3.76 ( 1466) hydrogen bonds : angle 4.16777 / 2.98 ( 4338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 386 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: A 27 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6745 (p-80) REVERT: A 81 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: C 1 MET cc_start: 0.5623 (mmp) cc_final: 0.5246 (mmm) REVERT: C 14 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: C 237 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5047 (t80) REVERT: D 60 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8273 (pp) REVERT: E 14 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: E 81 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: E 237 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5061 (t80) REVERT: G 14 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6556 (mt-10) REVERT: G 237 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.4996 (t80) outliers start: 84 outliers final: 34 residues processed: 431 average time/residue: 0.5482 time to fit residues: 279.7620 Evaluate side-chains 405 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 304 ARG Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 304 ARG Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [143, 297, 312, 189, 147, 149, 277, 271, 63, 171, 301] chunk 143 optimal weight: 4.9990 chunk 297 optimal weight: 0.2980 chunk 312 optimal weight: 2.9990 chunk 189 optimal weight: 0.0170 chunk 147 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 277 optimal weight: 0.6980 chunk 271 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.169488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152131 restraints weight = 33488.304| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.73 r_work: 0.3782 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26448 Z= 0.112 Angle : 0.503 8.095 35625 Z= 0.263 Chirality : 0.036 0.115 3873 Planarity : 0.003 0.030 4532 Dihedral : 11.118 162.408 3693 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.06 % Allowed : 24.19 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3183 helix: 1.64 (0.11), residues: 2137 sheet: None (None), residues: 0 loop : -0.93 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.018 0.001 TYR C 25 PHE 0.022 0.001 PHE D 185 HIS 0.011 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (26448) covalent geometry : angle 0.50254 / 0.26 (35625) hydrogen bonds : bond 0.04637 / 3.09 ( 1466) hydrogen bonds : angle 4.01350 / 2.87 ( 4338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 410 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: A 47 TYR cc_start: 0.8302 (m-80) cc_final: 0.8041 (m-80) REVERT: A 237 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5027 (t80) REVERT: C 1 MET cc_start: 0.5767 (mmp) cc_final: 0.5459 (mmm) REVERT: C 14 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: C 47 TYR cc_start: 0.8296 (m-80) cc_final: 0.8033 (m-80) REVERT: D 14 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: D 60 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8134 (pp) REVERT: E 14 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6507 (mt-10) REVERT: E 47 TYR cc_start: 0.8296 (m-80) cc_final: 0.8087 (m-80) REVERT: G 14 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: G 47 TYR cc_start: 0.8292 (m-80) cc_final: 0.8092 (m-80) outliers start: 84 outliers final: 24 residues processed: 452 average time/residue: 0.5255 time to fit residues: 282.7701 Evaluate side-chains 399 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 244 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [186, 263, 53, 284, 162, 289, 151, 36, 83, 122, 248] chunk 186 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150064 restraints weight = 33079.015| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.72 r_work: 0.3758 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26448 Z= 0.158 Angle : 0.542 7.022 35625 Z= 0.280 Chirality : 0.038 0.124 3873 Planarity : 0.003 0.033 4532 Dihedral : 11.191 166.956 3691 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.77 % Allowed : 23.43 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3183 helix: 1.54 (0.11), residues: 2137 sheet: None (None), residues: 0 loop : -1.02 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.017 0.001 TYR C 25 PHE 0.018 0.001 PHE F 185 HIS 0.006 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (26448) covalent geometry : angle 0.54163 / 0.28 (35625) hydrogen bonds : bond 0.05231 / 3.49 ( 1466) hydrogen bonds : angle 4.12202 / 2.96 ( 4338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 378 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: A 47 TYR cc_start: 0.8327 (m-80) cc_final: 0.8066 (m-80) REVERT: A 237 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5099 (t80) REVERT: C 1 MET cc_start: 0.5776 (mmp) cc_final: 0.5498 (mmm) REVERT: C 14 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: C 237 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5123 (t80) REVERT: D 14 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: E 14 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: E 237 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5085 (t80) REVERT: G 14 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: G 237 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5040 (t80) REVERT: G 273 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.5741 (t80) outliers start: 131 outliers final: 55 residues processed: 459 average time/residue: 0.5192 time to fit residues: 284.5228 Evaluate side-chains 428 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 363 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 273 TYR Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [67, 99, 226, 312, 2, 279, 122, 62, 301, 27, 51] chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150970 restraints weight = 33139.234| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.71 r_work: 0.3770 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26448 Z= 0.131 Angle : 0.524 6.987 35625 Z= 0.271 Chirality : 0.037 0.118 3873 Planarity : 0.003 0.032 4532 Dihedral : 11.209 169.469 3691 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.37 % Allowed : 23.83 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3183 helix: 1.69 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : -0.95 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.013 0.001 TYR G 47 PHE 0.015 0.001 PHE B 185 HIS 0.004 0.001 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (26448) covalent geometry : angle 0.52387 / 0.27 (35625) hydrogen bonds : bond 0.04819 / 3.21 ( 1466) hydrogen bonds : angle 4.08187 / 2.93 ( 4338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 385 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: A 27 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6772 (p-80) REVERT: A 237 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5140 (t80) REVERT: C 1 MET cc_start: 0.5739 (mmp) cc_final: 0.5477 (mmm) REVERT: C 14 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6285 (mt-10) REVERT: C 27 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.6703 (p-80) REVERT: C 47 TYR cc_start: 0.8278 (m-80) cc_final: 0.7994 (m-80) REVERT: C 237 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5154 (t80) REVERT: D 14 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: E 14 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: E 47 TYR cc_start: 0.8254 (m-80) cc_final: 0.7989 (m-80) REVERT: E 237 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5177 (t80) REVERT: G 14 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6358 (mt-10) REVERT: G 47 TYR cc_start: 0.8250 (m-80) cc_final: 0.7979 (m-80) REVERT: G 237 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5101 (t80) outliers start: 120 outliers final: 65 residues processed: 464 average time/residue: 0.4883 time to fit residues: 272.4010 Evaluate side-chains 438 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 362 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [233, 238, 148, 183, 272, 201, 292, 275, 219, 181, 221] chunk 233 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 221 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS B 93 ASN D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148600 restraints weight = 33238.002| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.73 r_work: 0.3744 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26448 Z= 0.192 Angle : 0.585 7.050 35625 Z= 0.300 Chirality : 0.039 0.127 3873 Planarity : 0.003 0.035 4532 Dihedral : 11.359 173.118 3691 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.95 % Allowed : 23.17 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3183 helix: 1.29 (0.11), residues: 2172 sheet: None (None), residues: 0 loop : -1.08 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.013 0.002 TYR C 214 PHE 0.015 0.002 PHE D 225 HIS 0.011 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (26448) covalent geometry : angle 0.58482 / 0.30 (35625) hydrogen bonds : bond 0.05616 / 3.74 ( 1466) hydrogen bonds : angle 4.26136 / 3.07 ( 4338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 383 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5736 (mmp) cc_final: 0.5389 (mmm) REVERT: A 14 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: A 237 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5110 (t80) REVERT: C 1 MET cc_start: 0.5743 (mmp) cc_final: 0.5483 (mmm) REVERT: C 14 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6396 (mt-10) REVERT: C 27 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: C 47 TYR cc_start: 0.8346 (m-80) cc_final: 0.8028 (m-80) REVERT: C 237 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5095 (t80) REVERT: D 14 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 14 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6455 (mt-10) REVERT: E 47 TYR cc_start: 0.8345 (m-80) cc_final: 0.8048 (m-80) REVERT: E 237 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5124 (t80) REVERT: G 14 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: G 47 TYR cc_start: 0.8314 (m-80) cc_final: 0.8017 (m-80) REVERT: G 237 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5089 (t80) REVERT: G 273 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.5755 (t80) REVERT: H 14 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7646 (tt0) outliers start: 136 outliers final: 68 residues processed: 479 average time/residue: 0.4667 time to fit residues: 269.8676 Evaluate side-chains 436 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 356 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 273 TYR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [72, 32, 22, 287, 101, 246, 271, 95, 316, 307, 139] chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 246 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 chunk 307 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 59 GLN G 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.150857 restraints weight = 33005.187| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.71 r_work: 0.3768 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26448 Z= 0.127 Angle : 0.536 7.779 35625 Z= 0.276 Chirality : 0.037 0.119 3873 Planarity : 0.003 0.031 4532 Dihedral : 11.325 173.677 3691 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.62 % Allowed : 23.86 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3183 helix: 1.54 (0.11), residues: 2131 sheet: None (None), residues: 0 loop : -0.96 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.016 0.001 TYR A 47 PHE 0.016 0.001 PHE H 185 HIS 0.006 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (26448) covalent geometry : angle 0.53581 / 0.28 (35625) hydrogen bonds : bond 0.04744 / 3.16 ( 1466) hydrogen bonds : angle 4.11101 / 2.96 ( 4338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 379 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5758 (mmp) cc_final: 0.5432 (mmm) REVERT: A 14 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: A 47 TYR cc_start: 0.8258 (m-80) cc_final: 0.7947 (m-80) REVERT: A 237 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5150 (t80) REVERT: C 14 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6413 (mt-10) REVERT: C 27 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6574 (p-80) REVERT: C 237 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5118 (t80) REVERT: D 14 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: E 14 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: G 14 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: H 14 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7641 (tt0) outliers start: 127 outliers final: 58 residues processed: 466 average time/residue: 0.4720 time to fit residues: 265.7840 Evaluate side-chains 425 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [231, 247, 290, 55, 152, 171, 197, 91, 282, 212, 291] chunk 231 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS B 93 ASN C 217 HIS D 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150091 restraints weight = 33323.254| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.73 r_work: 0.3758 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26448 Z= 0.151 Angle : 0.560 7.340 35625 Z= 0.289 Chirality : 0.038 0.121 3873 Planarity : 0.003 0.033 4532 Dihedral : 11.352 174.835 3691 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.26 % Allowed : 24.37 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3183 helix: 1.33 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : -0.99 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 70 TYR 0.014 0.001 TYR F 273 PHE 0.016 0.001 PHE D 185 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (26448) covalent geometry : angle 0.56022 / 0.29 (35625) hydrogen bonds : bond 0.05013 / 3.34 ( 1466) hydrogen bonds : angle 4.17997 / 3.01 ( 4338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 364 time to evaluate : 0.840 Fit side-chains REVERT: A 1 MET cc_start: 0.5699 (mmp) cc_final: 0.5380 (mmm) REVERT: A 14 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: A 237 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5097 (t80) REVERT: B 103 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8014 (mp) REVERT: C 14 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: C 237 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5080 (t80) REVERT: D 14 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: E 14 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: E 237 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5044 (t80) REVERT: F 103 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8048 (mp) REVERT: G 14 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6616 (mt-10) REVERT: G 47 TYR cc_start: 0.8278 (m-80) cc_final: 0.7957 (m-80) REVERT: G 237 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5005 (t80) REVERT: G 273 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.5777 (t80) REVERT: H 14 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7686 (tt0) outliers start: 117 outliers final: 62 residues processed: 448 average time/residue: 0.4773 time to fit residues: 258.0703 Evaluate side-chains 425 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 273 TYR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 393 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [297, 136, 256, 195, 213, 179, 279, 37, 36, 0, 152] chunk 297 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS C 217 HIS D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151486 restraints weight = 33261.821| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.70 r_work: 0.3775 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26448 Z= 0.127 Angle : 0.545 7.235 35625 Z= 0.282 Chirality : 0.037 0.119 3873 Planarity : 0.003 0.031 4532 Dihedral : 11.318 175.011 3691 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.93 % Allowed : 24.66 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3183 helix: 1.51 (0.11), residues: 2131 sheet: None (None), residues: 0 loop : -0.89 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 70 TYR 0.023 0.001 TYR A 183 PHE 0.018 0.001 PHE E 185 HIS 0.006 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26448) covalent geometry : angle 0.54477 / 0.28 (35625) hydrogen bonds : bond 0.04622 / 3.07 ( 1466) hydrogen bonds : angle 4.10942 / 2.96 ( 4338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 373 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5671 (mmp) cc_final: 0.5358 (mmm) REVERT: A 47 TYR cc_start: 0.8240 (m-80) cc_final: 0.7965 (m-80) REVERT: B 103 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7982 (mp) REVERT: C 14 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6446 (mt-10) REVERT: C 47 TYR cc_start: 0.8246 (m-80) cc_final: 0.7966 (m-80) REVERT: D 103 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7962 (mp) REVERT: E 14 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: E 47 TYR cc_start: 0.8228 (m-80) cc_final: 0.7953 (m-80) REVERT: E 237 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5115 (t80) REVERT: G 14 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: G 237 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5073 (t80) outliers start: 108 outliers final: 59 residues processed: 455 average time/residue: 0.4817 time to fit residues: 265.1909 Evaluate side-chains 418 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 381 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 393 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [36, 20, 273, 197, 233, 35, 56, 265, 296, 207, 29] chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 273 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 35 optimal weight: 0.0040 chunk 56 optimal weight: 0.2980 chunk 265 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS B 55 GLN B 217 HIS C 217 HIS D 55 GLN D 59 GLN H 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.171003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154003 restraints weight = 33196.850| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.69 r_work: 0.3808 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26448 Z= 0.104 Angle : 0.520 9.193 35625 Z= 0.271 Chirality : 0.036 0.202 3873 Planarity : 0.003 0.031 4532 Dihedral : 11.180 173.370 3691 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 26.88 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3183 helix: 1.64 (0.12), residues: 2124 sheet: None (None), residues: 0 loop : -0.85 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 70 TYR 0.018 0.001 TYR G 47 PHE 0.019 0.001 PHE D 185 HIS 0.006 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (26448) covalent geometry : angle 0.51971 / 0.27 (35625) hydrogen bonds : bond 0.03934 / 2.62 ( 1466) hydrogen bonds : angle 3.99670 / 2.88 ( 4338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 408 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5581 (mmp) cc_final: 0.5294 (mmm) REVERT: C 1 MET cc_start: 0.5609 (mmp) cc_final: 0.5212 (mmm) REVERT: C 207 ASP cc_start: 0.7165 (t70) cc_final: 0.6920 (m-30) REVERT: F 61 LEU cc_start: 0.6905 (mm) cc_final: 0.6423 (pt) REVERT: G 14 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: G 47 TYR cc_start: 0.8195 (m-80) cc_final: 0.7911 (m-80) REVERT: G 175 LYS cc_start: 0.8274 (mppt) cc_final: 0.7872 (mptp) REVERT: G 207 ASP cc_start: 0.7070 (t70) cc_final: 0.6776 (m-30) outliers start: 61 outliers final: 34 residues processed: 458 average time/residue: 0.4939 time to fit residues: 271.9580 Evaluate side-chains 411 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 366 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 393 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: [153, 211, 174, 40, 61, 93, 182, 132, 56, 294, 288] chunk 153 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 174 optimal weight: 0.0980 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS B 93 ASN B 135 GLN C 217 HIS D 59 GLN F 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151410 restraints weight = 33185.939| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.70 r_work: 0.3776 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26448 Z= 0.146 Angle : 0.566 8.360 35625 Z= 0.294 Chirality : 0.038 0.204 3873 Planarity : 0.003 0.031 4532 Dihedral : 11.225 174.777 3689 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.73 % Allowed : 26.81 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3183 helix: 1.45 (0.11), residues: 2130 sheet: None (None), residues: 0 loop : -0.89 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 70 TYR 0.021 0.001 TYR E 47 PHE 0.028 0.002 PHE E 225 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (26448) covalent geometry : angle 0.56628 / 0.29 (35625) hydrogen bonds : bond 0.04748 / 3.16 ( 1466) hydrogen bonds : angle 4.14720 / 2.98 ( 4338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7751.18 seconds wall clock time: 132 minutes 55.46 seconds (7975.46 seconds total)