Starting phenix.real_space_refine on Wed Mar 4 16:04:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sng_25225/03_2026/7sng_25225.map" } resolution = 2.8 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= 0.012 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9632 2.51 5 N 2616 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 residue: pdb=" N GLU C 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C 504 " occ=0.50 residue: pdb=" N GLU D 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D 504 " occ=0.50 Time building chain proxies: 3.69, per 1000 atoms: 0.24 Number of scatterers: 15204 At special positions: 0 Unit cell: (135.29, 96.28, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2876 8.00 N 2616 7.00 C 9632 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: 1.25 Conformation dependent library (CDL) restraints added in 682.6 milliseconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 43.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.793A pdb=" N PHE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.735A pdb=" N HIS A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.546A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.746A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.282A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.717A pdb=" N GLU A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.645A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.572A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.891A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 3.810A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.585A pdb=" N TYR B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.809A pdb=" N ASN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.745A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.623A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.531A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.550A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.080A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 47 through 58 Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 3.837A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.612A pdb=" N TYR C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.757A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.250A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.502A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.562A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.042A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 47 through 58 Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.873A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.534A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.692A pdb=" N TYR D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.805A pdb=" N ASN D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.541A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.294A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.521A pdb=" N GLN D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.695A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.604A pdb=" N THR D 319 " --> pdb=" O GLY D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.534A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.046A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.418A pdb=" N ILE A 33 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.449A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 232 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.491A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 421 removed outlier: 6.699A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 232 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.420A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.760A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS C 232 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ILE C 480 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 305 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR C 482 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN C 307 " --> pdb=" O TYR C 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.485A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.719A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 232 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE D 480 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 305 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR D 482 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN D 307 " --> pdb=" O TYR D 482 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1839 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: 2.51 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2534 1.32 - 1.44: 4163 1.44 - 1.57: 8623 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA LYS D 171 " pdb=" C LYS D 171 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.11e-02 8.12e+03 2.11e+01 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.17e-02 7.31e+03 1.97e+01 bond pdb=" N VAL D 169 " pdb=" CA VAL D 169 " ideal model delta sigma weight residual 1.458 1.407 0.051 1.20e-02 6.94e+03 1.81e+01 bond pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.07e-02 8.73e+03 1.75e+01 bond pdb=" C VAL D 169 " pdb=" O VAL D 169 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.13e-02 7.83e+03 1.47e+01 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 20571 2.20 - 4.41: 280 4.41 - 6.61: 32 6.61 - 8.81: 11 8.81 - 11.02: 2 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 314 " pdb=" CA GLY B 314 " pdb=" C GLY B 314 " ideal model delta sigma weight residual 111.85 117.84 -5.99 1.06e+00 8.90e-01 3.19e+01 angle pdb=" C ASN B 311 " pdb=" N PRO B 312 " pdb=" CA PRO B 312 " ideal model delta sigma weight residual 119.24 113.54 5.70 1.04e+00 9.25e-01 3.00e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" CB GLU D 170 " ideal model delta sigma weight residual 110.85 102.56 8.29 1.60e+00 3.91e-01 2.69e+01 angle pdb=" N GLY B 316 " pdb=" CA GLY B 316 " pdb=" C GLY B 316 " ideal model delta sigma weight residual 113.18 102.16 11.02 2.37e+00 1.78e-01 2.16e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" C GLU D 170 " ideal model delta sigma weight residual 109.95 116.96 -7.01 1.59e+00 3.96e-01 1.94e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8413 17.98 - 35.97: 700 35.97 - 53.95: 135 53.95 - 71.93: 39 71.93 - 89.91: 17 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA MET D 411 " pdb=" C MET D 411 " pdb=" N PHE D 412 " pdb=" CA PHE D 412 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET A 411 " pdb=" C MET A 411 " pdb=" N PHE A 412 " pdb=" CA PHE A 412 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET C 411 " pdb=" C MET C 411 " pdb=" N PHE C 412 " pdb=" CA PHE C 412 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1539 0.040 - 0.080: 496 0.080 - 0.120: 168 0.120 - 0.159: 35 0.159 - 0.199: 2 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA VAL B 309 " pdb=" N VAL B 309 " pdb=" C VAL B 309 " pdb=" CB VAL B 309 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CB VAL D 169 " pdb=" CA VAL D 169 " pdb=" CG1 VAL D 169 " pdb=" CG2 VAL D 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 311 " -0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 312 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO D 312 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 225 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP D 225 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 225 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP D 225 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 225 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 225 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 225 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 225 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 225 " -0.002 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1341 2.74 - 3.28: 15171 3.28 - 3.82: 26513 3.82 - 4.36: 34513 4.36 - 4.90: 56961 Nonbonded interactions: 134499 Sorted by model distance: nonbonded pdb=" O LYS A 47 " pdb=" OG1 THR A 51 " model vdw 2.201 3.040 nonbonded pdb=" O LYS C 47 " pdb=" OG1 THR C 51 " model vdw 2.205 3.040 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.208 3.120 nonbonded pdb=" O LYS D 47 " pdb=" OG1 THR D 51 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.218 3.040 ... (remaining 134494 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.066 15452 Z= 0.210 Angle : 0.634 11.017 20896 Z= 0.341 Chirality : 0.045 0.199 2240 Planarity : 0.006 0.098 2732 Dihedral : 14.539 89.913 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 0.25 % Allowed : 0.31 % Favored : 99.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 8.70 % 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: -0.68 (0.20), residues: 1852 helix: -0.33 (0.21), residues: 684 sheet: -0.80 (0.24), residues: 412 loop : -0.09 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.038 0.001 TYR D 139 PHE 0.017 0.001 PHE D 413 TRP 0.050 0.003 TRP D 225 HIS 0.002 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00403 (15452) covalent geometry : angle 0.63405 (20896) hydrogen bonds : bond 0.15238 ( 636) hydrogen bonds : angle 7.62415 ( 1839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 0.627 Fit side-chains REVERT: C 37 MET cc_start: 0.9070 (mmm) cc_final: 0.8834 (mmt) REVERT: D 244 GLU cc_start: 0.7737 (mp0) cc_final: 0.7516 (mp0) outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 0.7129 time to fit residues: 186.3743 Evaluate side-chains 197 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain D residue 171 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN B 383 GLN C 83 GLN C 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130440 restraints weight = 16747.759| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.62 r_work: 0.3325 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15452 Z= 0.283 Angle : 0.687 12.845 20896 Z= 0.352 Chirality : 0.049 0.163 2240 Planarity : 0.006 0.071 2732 Dihedral : 5.194 39.626 2061 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 1.41 % Allowed : 8.09 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.60 (0.19), residues: 1852 helix: -0.01 (0.20), residues: 708 sheet: -0.91 (0.24), residues: 408 loop : -0.22 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 120 TYR 0.033 0.002 TYR D 139 PHE 0.025 0.002 PHE D 413 TRP 0.021 0.003 TRP D 225 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00676 (15452) covalent geometry : angle 0.68732 (20896) hydrogen bonds : bond 0.04724 ( 636) hydrogen bonds : angle 5.83517 ( 1839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.545 Fit side-chains REVERT: A 258 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (t70) REVERT: A 503 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 249 TYR cc_start: 0.8119 (m-10) cc_final: 0.7860 (m-10) REVERT: D 389 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8216 (mt-10) outliers start: 23 outliers final: 10 residues processed: 234 average time/residue: 0.6806 time to fit residues: 173.5880 Evaluate side-chains 218 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN C 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134039 restraints weight = 16875.695| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.64 r_work: 0.3372 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15452 Z= 0.148 Angle : 0.556 6.660 20896 Z= 0.289 Chirality : 0.044 0.148 2240 Planarity : 0.004 0.062 2732 Dihedral : 4.657 27.303 2057 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.35 % Allowed : 11.52 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.31 (0.20), residues: 1852 helix: 0.30 (0.20), residues: 712 sheet: -0.74 (0.26), residues: 368 loop : -0.21 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 120 TYR 0.016 0.001 TYR D 139 PHE 0.013 0.001 PHE D 413 TRP 0.016 0.002 TRP B 164 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00346 (15452) covalent geometry : angle 0.55575 (20896) hydrogen bonds : bond 0.03740 ( 636) hydrogen bonds : angle 5.38687 ( 1839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 0.496 Fit side-chains REVERT: A 258 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7855 (t70) REVERT: A 383 GLN cc_start: 0.8112 (mp-120) cc_final: 0.7901 (mm-40) REVERT: A 503 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 503 TYR cc_start: 0.7568 (t80) cc_final: 0.7339 (t80) REVERT: D 389 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: D 473 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7176 (mm-30) outliers start: 22 outliers final: 7 residues processed: 250 average time/residue: 0.7066 time to fit residues: 192.2153 Evaluate side-chains 230 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 384 GLN A 414 ASN B 83 GLN B 451 HIS C 451 HIS D 414 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129865 restraints weight = 15997.825| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.00 r_work: 0.3166 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15452 Z= 0.139 Angle : 0.542 6.288 20896 Z= 0.281 Chirality : 0.043 0.146 2240 Planarity : 0.004 0.057 2732 Dihedral : 4.496 20.524 2057 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.35 % Allowed : 15.07 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.22 (0.20), residues: 1852 helix: 0.45 (0.20), residues: 716 sheet: -0.78 (0.25), residues: 400 loop : -0.15 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 120 TYR 0.012 0.001 TYR D 139 PHE 0.015 0.001 PHE D 102 TRP 0.015 0.002 TRP D 53 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00323 (15452) covalent geometry : angle 0.54199 (20896) hydrogen bonds : bond 0.03511 ( 636) hydrogen bonds : angle 5.18495 ( 1839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.637 Fit side-chains REVERT: A 258 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7785 (t70) REVERT: C 142 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (pt) REVERT: C 244 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: D 389 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: D 473 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7134 (mm-30) outliers start: 22 outliers final: 9 residues processed: 237 average time/residue: 0.7054 time to fit residues: 182.1430 Evaluate side-chains 227 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 83 GLN C 451 HIS D 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134887 restraints weight = 15935.530| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.96 r_work: 0.3199 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15452 Z= 0.112 Angle : 0.517 5.611 20896 Z= 0.269 Chirality : 0.043 0.148 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.325 19.820 2056 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.53 % Allowed : 16.61 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.02 (0.20), residues: 1852 helix: 0.61 (0.20), residues: 716 sheet: -0.48 (0.27), residues: 356 loop : -0.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.013 0.001 TYR A 249 PHE 0.015 0.001 PHE C 87 TRP 0.016 0.002 TRP B 53 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00255 (15452) covalent geometry : angle 0.51659 (20896) hydrogen bonds : bond 0.03256 ( 636) hydrogen bonds : angle 4.98433 ( 1839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.613 Fit side-chains REVERT: A 104 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7360 (tpt-90) REVERT: A 368 GLU cc_start: 0.8947 (pt0) cc_final: 0.8746 (pt0) REVERT: C 244 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6627 (pm20) REVERT: D 389 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: D 473 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6968 (mp0) outliers start: 25 outliers final: 12 residues processed: 238 average time/residue: 0.6929 time to fit residues: 180.0608 Evaluate side-chains 228 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 6 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 451 HIS C 451 HIS D 414 ASN D 470 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128058 restraints weight = 15916.319| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.06 r_work: 0.3098 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15452 Z= 0.267 Angle : 0.646 8.444 20896 Z= 0.328 Chirality : 0.047 0.156 2240 Planarity : 0.005 0.051 2732 Dihedral : 4.771 21.290 2056 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 17.10 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.33 (0.19), residues: 1852 helix: 0.29 (0.20), residues: 712 sheet: -0.88 (0.24), residues: 440 loop : -0.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 175 TYR 0.016 0.002 TYR A 401 PHE 0.021 0.002 PHE C 413 TRP 0.019 0.003 TRP A 53 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00641 (15452) covalent geometry : angle 0.64567 (20896) hydrogen bonds : bond 0.04228 ( 636) hydrogen bonds : angle 5.38278 ( 1839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.545 Fit side-chains REVERT: A 104 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7364 (tpt90) REVERT: A 414 ASN cc_start: 0.8249 (m110) cc_final: 0.7994 (m-40) REVERT: B 175 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7687 (mtp85) REVERT: B 503 TYR cc_start: 0.7877 (t80) cc_final: 0.7434 (t80) REVERT: D 389 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: D 473 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7101 (mm-30) outliers start: 31 outliers final: 12 residues processed: 233 average time/residue: 0.6636 time to fit residues: 168.8128 Evaluate side-chains 221 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 83 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN C 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134595 restraints weight = 15741.113| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.85 r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15452 Z= 0.109 Angle : 0.524 6.213 20896 Z= 0.273 Chirality : 0.043 0.148 2240 Planarity : 0.004 0.051 2732 Dihedral : 4.347 18.254 2056 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 1.53 % Allowed : 18.57 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1852 helix: 0.63 (0.20), residues: 716 sheet: -0.73 (0.25), residues: 400 loop : -0.10 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 120 TYR 0.013 0.001 TYR A 249 PHE 0.012 0.001 PHE C 102 TRP 0.024 0.002 TRP A 53 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00245 (15452) covalent geometry : angle 0.52405 (20896) hydrogen bonds : bond 0.03190 ( 636) hydrogen bonds : angle 4.98773 ( 1839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.399 Fit side-chains REVERT: C 404 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8113 (mtm) REVERT: D 473 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7135 (mm-30) outliers start: 25 outliers final: 11 residues processed: 230 average time/residue: 0.6532 time to fit residues: 164.3787 Evaluate side-chains 224 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134792 restraints weight = 15889.289| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.92 r_work: 0.3211 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15452 Z= 0.113 Angle : 0.521 6.381 20896 Z= 0.271 Chirality : 0.043 0.147 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.261 19.071 2056 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.29 % Allowed : 19.06 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.14 (0.20), residues: 1852 helix: 0.69 (0.20), residues: 716 sheet: -0.43 (0.27), residues: 364 loop : -0.03 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 120 TYR 0.013 0.001 TYR A 249 PHE 0.017 0.001 PHE C 87 TRP 0.028 0.002 TRP A 53 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00260 (15452) covalent geometry : angle 0.52145 (20896) hydrogen bonds : bond 0.03162 ( 636) hydrogen bonds : angle 4.86714 ( 1839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.560 Fit side-chains REVERT: A 104 ARG cc_start: 0.7583 (tpt90) cc_final: 0.7374 (tpt-90) REVERT: D 389 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (mt-10) outliers start: 21 outliers final: 12 residues processed: 227 average time/residue: 0.6539 time to fit residues: 163.0826 Evaluate side-chains 224 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 83 GLN B 383 GLN C 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131475 restraints weight = 15825.603| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.02 r_work: 0.3179 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15452 Z= 0.147 Angle : 0.556 7.392 20896 Z= 0.286 Chirality : 0.044 0.146 2240 Planarity : 0.004 0.049 2732 Dihedral : 4.369 19.561 2056 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 1.23 % Allowed : 19.00 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.03 (0.20), residues: 1852 helix: 0.65 (0.20), residues: 716 sheet: -0.82 (0.24), residues: 456 loop : 0.10 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 120 TYR 0.016 0.001 TYR A 249 PHE 0.012 0.001 PHE C 413 TRP 0.031 0.002 TRP B 53 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00348 (15452) covalent geometry : angle 0.55649 (20896) hydrogen bonds : bond 0.03391 ( 636) hydrogen bonds : angle 4.94373 ( 1839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.712 Fit side-chains REVERT: A 104 ARG cc_start: 0.7525 (tpt90) cc_final: 0.7306 (tpt-90) REVERT: A 258 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7762 (t70) REVERT: A 412 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6269 (p90) REVERT: B 252 GLU cc_start: 0.7790 (mp0) cc_final: 0.7362 (mp0) REVERT: C 320 LYS cc_start: 0.8376 (mppt) cc_final: 0.8113 (mptt) REVERT: D 389 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8284 (mt-10) outliers start: 20 outliers final: 14 residues processed: 226 average time/residue: 0.6777 time to fit residues: 167.3464 Evaluate side-chains 224 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130903 restraints weight = 15981.968| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.08 r_work: 0.3179 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15452 Z= 0.157 Angle : 0.569 7.258 20896 Z= 0.291 Chirality : 0.044 0.146 2240 Planarity : 0.004 0.058 2732 Dihedral : 4.424 19.605 2056 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 0.98 % Allowed : 19.55 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.02 (0.20), residues: 1852 helix: 0.62 (0.20), residues: 720 sheet: -0.79 (0.24), residues: 456 loop : 0.15 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 120 TYR 0.017 0.001 TYR A 249 PHE 0.012 0.001 PHE C 413 TRP 0.035 0.002 TRP A 53 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00372 (15452) covalent geometry : angle 0.56919 (20896) hydrogen bonds : bond 0.03471 ( 636) hydrogen bonds : angle 5.00982 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.649 Fit side-chains REVERT: A 104 ARG cc_start: 0.7550 (tpt90) cc_final: 0.7321 (tpt-90) REVERT: A 258 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7794 (t70) REVERT: C 320 LYS cc_start: 0.8400 (mppt) cc_final: 0.8130 (mptt) REVERT: D 389 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8114 (mt-10) outliers start: 16 outliers final: 14 residues processed: 229 average time/residue: 0.6632 time to fit residues: 166.4624 Evaluate side-chains 227 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.0970 chunk 152 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN C 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134225 restraints weight = 15791.172| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15452 Z= 0.122 Angle : 0.545 8.013 20896 Z= 0.280 Chirality : 0.043 0.144 2240 Planarity : 0.004 0.058 2732 Dihedral : 4.294 18.525 2056 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 1.16 % Allowed : 19.61 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1852 helix: 0.71 (0.20), residues: 716 sheet: -0.61 (0.24), residues: 444 loop : 0.05 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 120 TYR 0.017 0.001 TYR A 249 PHE 0.009 0.001 PHE C 102 TRP 0.035 0.002 TRP B 53 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00281 (15452) covalent geometry : angle 0.54506 (20896) hydrogen bonds : bond 0.03205 ( 636) hydrogen bonds : angle 4.88252 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5967.74 seconds wall clock time: 102 minutes 14.42 seconds (6134.42 seconds total)