Starting phenix.real_space_refine on Tue Dec 31 03:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030.map" model { file = "/net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toe_26030/12_2024/7toe_26030_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.163 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 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15100 Number of models: 1 Model: "" Number of chains: 4 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 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: 8.91, per 1000 atoms: 0.59 Number of scatterers: 15100 At special positions: 0 Unit cell: (135.29, 95.45, 117.03, 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 2772 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: 3.88 Conformation dependent library (CDL) restraints added in 2.4 seconds 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 43.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 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 89 removed outlier: 3.940A pdb=" N LYS A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' 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 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.554A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.561A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.638A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.407A 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: 3.818A 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: 3.647A 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: 3.689A 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 58 removed outlier: 5.513A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 4.017A 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 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.550A 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 217 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.799A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.237A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.743A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (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 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.601A 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: 3.993A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.395A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 4.191A 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 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.695A 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: 3.549A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.272A 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: 3.662A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.561A 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 Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.504A 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: 4.041A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.450A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.938A 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 104 removed outlier: 3.700A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.719A 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 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.506A 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 217 Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.923A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 4.225A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.526A 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 Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.614A 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: 3.880A 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: 7.968A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.414A 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: 6.451A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 7.950A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.507A 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: 6.651A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.317A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.574A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.274A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.620A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2647 1.32 - 1.44: 4056 1.44 - 1.57: 8617 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA PRO A 50 " pdb=" CB PRO A 50 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA ILE B 464 " pdb=" C ILE B 464 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.27e-02 6.20e+03 1.38e+01 bond pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.39e-02 5.18e+03 1.05e+01 bond pdb=" C ILE B 464 " pdb=" O ILE B 464 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.19e-02 7.06e+03 9.19e+00 bond pdb=" CA TRP B 462 " pdb=" CB TRP B 462 " ideal model delta sigma weight residual 1.532 1.489 0.044 1.53e-02 4.27e+03 8.14e+00 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 20285 1.48 - 2.96: 498 2.96 - 4.43: 80 4.43 - 5.91: 26 5.91 - 7.39: 7 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 310 " pdb=" CA GLY B 310 " pdb=" C GLY B 310 " ideal model delta sigma weight residual 111.36 118.56 -7.20 1.17e+00 7.31e-01 3.79e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 112.35 104.96 7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta sigma weight residual 119.28 113.94 5.34 1.10e+00 8.26e-01 2.36e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 112.38 107.59 4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N TRP B 462 " pdb=" CA TRP B 462 " pdb=" C TRP B 462 " ideal model delta sigma weight residual 113.41 108.66 4.75 1.22e+00 6.72e-01 1.51e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8445 17.87 - 35.74: 683 35.74 - 53.62: 125 53.62 - 71.49: 38 71.49 - 89.36: 13 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N CYS A 158 " pdb=" CA CYS A 158 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER D 157 " pdb=" C SER D 157 " pdb=" N CYS D 158 " pdb=" CA CYS D 158 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 259 " pdb=" C VAL A 259 " pdb=" N MET A 260 " pdb=" CA MET A 260 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1716 0.046 - 0.093: 383 0.093 - 0.139: 139 0.139 - 0.186: 1 0.186 - 0.232: 1 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLN A 119 " pdb=" N GLN A 119 " pdb=" C GLN A 119 " pdb=" CB GLN A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA GLU C 473 " pdb=" N GLU C 473 " pdb=" C GLU C 473 " pdb=" CB GLU C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 312 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 49 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 50 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.020 2.00e-02 2.50e+03 1.75e-02 6.13e+00 pdb=" CG TYR B 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.005 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1218 2.74 - 3.28: 14964 3.28 - 3.82: 25676 3.82 - 4.36: 32498 4.36 - 4.90: 55183 Nonbonded interactions: 129539 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" OE2 GLU A 170 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" OH TYR A 437 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 139 " pdb=" OH TYR C 437 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.232 3.120 nonbonded pdb=" O LYS B 47 " pdb=" OG1 THR B 51 " model vdw 2.234 3.040 ... (remaining 129534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.320 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.062 15452 Z= 0.209 Angle : 0.588 7.388 20896 Z= 0.327 Chirality : 0.043 0.232 2240 Planarity : 0.004 0.063 2732 Dihedral : 14.035 89.359 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1852 helix: 0.24 (0.20), residues: 704 sheet: -0.60 (0.23), residues: 444 loop : 0.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 225 HIS 0.003 0.001 HIS D 451 PHE 0.021 0.001 PHE C 88 TYR 0.041 0.002 TYR B 139 ARG 0.008 0.000 ARG D 439 *********************** 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 292 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 1.658 Fit side-chains REVERT: B 30 ASP cc_start: 0.7179 (t0) cc_final: 0.6711 (OUTLIER) REVERT: B 121 LEU cc_start: 0.8476 (tt) cc_final: 0.8273 (tm) REVERT: B 130 LEU cc_start: 0.8312 (tp) cc_final: 0.8079 (tp) REVERT: B 171 LYS cc_start: 0.7717 (ptmm) cc_final: 0.7397 (pttp) REVERT: B 249 TYR cc_start: 0.7017 (t80) cc_final: 0.6789 (t80) REVERT: B 446 CYS cc_start: 0.7767 (m) cc_final: 0.7461 (m) REVERT: B 497 LYS cc_start: 0.8358 (tptt) cc_final: 0.7998 (tttp) REVERT: D 37 MET cc_start: 0.8817 (mmm) cc_final: 0.8563 (mmt) REVERT: D 140 LEU cc_start: 0.8260 (mp) cc_final: 0.8015 (mt) outliers start: 2 outliers final: 3 residues processed: 292 average time/residue: 1.3117 time to fit residues: 422.7971 Evaluate side-chains 189 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15452 Z= 0.231 Angle : 0.586 8.200 20896 Z= 0.306 Chirality : 0.045 0.208 2240 Planarity : 0.005 0.053 2732 Dihedral : 4.557 57.413 2060 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.29 % Allowed : 10.11 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1852 helix: 0.47 (0.20), residues: 692 sheet: -0.58 (0.24), residues: 408 loop : -0.18 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 PHE 0.018 0.001 PHE C 241 TYR 0.021 0.001 TYR B 139 ARG 0.006 0.000 ARG D 459 *********************** 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 233 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.670 Fit side-chains REVERT: A 152 LYS cc_start: 0.7294 (tmmt) cc_final: 0.7059 (tttt) REVERT: B 30 ASP cc_start: 0.7245 (t0) cc_final: 0.6711 (OUTLIER) REVERT: B 130 LEU cc_start: 0.8310 (tp) cc_final: 0.8055 (tp) REVERT: B 171 LYS cc_start: 0.7690 (ptmm) cc_final: 0.7379 (pttp) REVERT: B 249 TYR cc_start: 0.7032 (t80) cc_final: 0.6789 (t80) REVERT: B 389 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: B 446 CYS cc_start: 0.7710 (m) cc_final: 0.7460 (m) REVERT: B 497 LYS cc_start: 0.8349 (tptt) cc_final: 0.7983 (tttp) REVERT: C 130 LEU cc_start: 0.8585 (tp) cc_final: 0.8283 (tt) REVERT: C 405 MET cc_start: 0.7929 (mmm) cc_final: 0.7117 (mmt) REVERT: C 475 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 37 MET cc_start: 0.8673 (mmm) cc_final: 0.8213 (mmt) REVERT: D 95 LYS cc_start: 0.7677 (tmmt) cc_final: 0.7032 (tmmt) REVERT: D 99 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: D 135 ASN cc_start: 0.8326 (m-40) cc_final: 0.8055 (m110) REVERT: D 140 LEU cc_start: 0.8194 (mp) cc_final: 0.7907 (mt) outliers start: 21 outliers final: 12 residues processed: 227 average time/residue: 1.1662 time to fit residues: 295.7287 Evaluate side-chains 202 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 493 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN D 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.005 0.044 15452 Z= 0.323 Angle : 0.604 7.649 20896 Z= 0.311 Chirality : 0.045 0.187 2240 Planarity : 0.005 0.053 2732 Dihedral : 4.462 19.793 2056 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.33 % Allowed : 12.56 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1852 helix: 0.28 (0.20), residues: 720 sheet: -0.83 (0.23), residues: 432 loop : -0.17 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 53 HIS 0.004 0.001 HIS A 124 PHE 0.017 0.002 PHE B 102 TYR 0.019 0.002 TYR B 139 ARG 0.006 0.000 ARG D 459 *********************** 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 245 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.799 Fit side-chains REVERT: A 152 LYS cc_start: 0.7204 (tmmt) cc_final: 0.7004 (tttt) REVERT: A 159 MET cc_start: 0.7582 (tpp) cc_final: 0.7315 (tpp) REVERT: A 175 ARG cc_start: 0.7972 (ptm160) cc_final: 0.7501 (ptm160) REVERT: A 258 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7693 (t70) REVERT: B 30 ASP cc_start: 0.7383 (t0) cc_final: 0.6811 (OUTLIER) REVERT: B 97 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7162 (ttpp) REVERT: B 249 TYR cc_start: 0.7037 (t80) cc_final: 0.6794 (t80) REVERT: B 389 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: B 395 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: B 446 CYS cc_start: 0.7780 (m) cc_final: 0.7476 (m) REVERT: B 497 LYS cc_start: 0.8342 (tptt) cc_final: 0.7970 (tttp) REVERT: C 317 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: C 475 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 37 MET cc_start: 0.8616 (mmm) cc_final: 0.7848 (mmt) REVERT: D 66 PHE cc_start: 0.8147 (m-80) cc_final: 0.7909 (m-80) REVERT: D 95 LYS cc_start: 0.7571 (tmmt) cc_final: 0.7021 (tmmt) REVERT: D 99 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: D 135 ASN cc_start: 0.8374 (m-40) cc_final: 0.8148 (m110) outliers start: 38 outliers final: 17 residues processed: 234 average time/residue: 1.2482 time to fit residues: 324.2294 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 493 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 0.0370 chunk 177 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15452 Z= 0.261 Angle : 0.577 8.547 20896 Z= 0.297 Chirality : 0.044 0.188 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.434 19.261 2056 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 2.14 % Allowed : 15.07 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1852 helix: 0.41 (0.20), residues: 720 sheet: -0.88 (0.23), residues: 444 loop : -0.09 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.004 0.001 HIS A 124 PHE 0.019 0.001 PHE C 241 TYR 0.019 0.001 TYR A 308 ARG 0.007 0.000 ARG D 459 *********************** 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 245 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7364 (ttp-110) REVERT: A 159 MET cc_start: 0.7604 (tpp) cc_final: 0.7305 (tpp) REVERT: A 258 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7684 (t70) REVERT: B 249 TYR cc_start: 0.7035 (t80) cc_final: 0.6771 (t80) REVERT: B 389 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: B 395 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: B 446 CYS cc_start: 0.7788 (m) cc_final: 0.7509 (m) REVERT: B 497 LYS cc_start: 0.8329 (tptt) cc_final: 0.7968 (tttp) REVERT: C 89 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8387 (mptt) REVERT: C 130 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 317 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6223 (tt0) REVERT: C 466 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (m) REVERT: C 475 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 37 MET cc_start: 0.8609 (mmm) cc_final: 0.7822 (mmt) REVERT: D 95 LYS cc_start: 0.7470 (tmmt) cc_final: 0.7002 (tmmt) REVERT: D 99 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6921 (mp0) outliers start: 35 outliers final: 17 residues processed: 234 average time/residue: 1.2845 time to fit residues: 332.9750 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 493 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 159 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15452 Z= 0.302 Angle : 0.593 7.891 20896 Z= 0.304 Chirality : 0.045 0.194 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.476 18.804 2056 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.76 % Allowed : 16.54 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1852 helix: 0.28 (0.19), residues: 744 sheet: -0.97 (0.22), residues: 452 loop : -0.03 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 PHE 0.018 0.001 PHE A 253 TYR 0.018 0.002 TYR A 308 ARG 0.007 0.000 ARG D 459 *********************** 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 249 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7637 (tpp) cc_final: 0.7323 (tpp) REVERT: A 258 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (t70) REVERT: B 130 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8016 (tm) REVERT: B 249 TYR cc_start: 0.7048 (t80) cc_final: 0.6843 (t80) REVERT: B 258 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 389 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: B 395 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: B 446 CYS cc_start: 0.7692 (m) cc_final: 0.7360 (m) REVERT: B 497 LYS cc_start: 0.8290 (tptt) cc_final: 0.7917 (tttp) REVERT: C 89 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8403 (mptt) REVERT: C 120 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7568 (ptp90) REVERT: C 130 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 166 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7136 (mtp85) REVERT: C 317 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: C 466 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8135 (m) REVERT: C 475 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 37 MET cc_start: 0.8582 (mmm) cc_final: 0.7858 (mmt) REVERT: D 66 PHE cc_start: 0.8142 (m-80) cc_final: 0.7938 (m-80) outliers start: 45 outliers final: 18 residues processed: 236 average time/residue: 1.2225 time to fit residues: 321.2138 Evaluate side-chains 219 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 414 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN C 451 HIS D 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15452 Z= 0.316 Angle : 0.602 7.480 20896 Z= 0.307 Chirality : 0.045 0.195 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.515 18.665 2056 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 3.06 % Allowed : 17.40 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1852 helix: 0.37 (0.19), residues: 732 sheet: -1.02 (0.22), residues: 452 loop : -0.09 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 PHE 0.020 0.001 PHE C 56 TYR 0.018 0.002 TYR A 308 ARG 0.008 0.000 ARG D 459 *********************** 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 255 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: A 159 MET cc_start: 0.7656 (tpp) cc_final: 0.7361 (tpp) REVERT: A 258 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7679 (t70) REVERT: A 411 MET cc_start: 0.6850 (mtt) cc_final: 0.6279 (mtt) REVERT: B 130 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8037 (tm) REVERT: B 258 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: B 389 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: B 395 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: B 446 CYS cc_start: 0.7709 (m) cc_final: 0.7364 (m) REVERT: B 497 LYS cc_start: 0.8304 (tptt) cc_final: 0.7939 (tttp) REVERT: C 89 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8420 (mptt) REVERT: C 120 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7545 (ptp90) REVERT: C 130 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8198 (tt) REVERT: C 166 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7183 (mtp85) REVERT: C 317 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: C 466 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8146 (m) REVERT: C 475 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 37 MET cc_start: 0.8594 (mmm) cc_final: 0.7941 (mmt) REVERT: D 66 PHE cc_start: 0.8056 (m-80) cc_final: 0.7606 (m-80) outliers start: 50 outliers final: 21 residues processed: 241 average time/residue: 1.2303 time to fit residues: 328.9653 Evaluate side-chains 221 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15452 Z= 0.296 Angle : 0.598 7.654 20896 Z= 0.305 Chirality : 0.044 0.204 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.494 18.520 2056 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 2.63 % Allowed : 18.44 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1852 helix: 0.40 (0.19), residues: 732 sheet: -1.08 (0.22), residues: 440 loop : -0.14 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 53 HIS 0.004 0.001 HIS D 451 PHE 0.025 0.001 PHE C 56 TYR 0.018 0.002 TYR A 308 ARG 0.009 0.000 ARG D 459 *********************** 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 243 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7482 (ttp-110) REVERT: A 93 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: A 159 MET cc_start: 0.7622 (tpp) cc_final: 0.7324 (tpp) REVERT: A 176 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: A 258 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7669 (t70) REVERT: B 258 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: B 389 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: B 411 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.3465 (mpt) REVERT: B 446 CYS cc_start: 0.7712 (m) cc_final: 0.7378 (m) REVERT: B 497 LYS cc_start: 0.8261 (tptt) cc_final: 0.7896 (tttp) REVERT: C 89 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8450 (mptt) REVERT: C 120 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7562 (ptp90) REVERT: C 130 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 166 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: C 317 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6280 (tt0) REVERT: C 466 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (m) REVERT: C 475 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 37 MET cc_start: 0.8589 (mmm) cc_final: 0.7962 (mmt) REVERT: D 66 PHE cc_start: 0.8074 (m-80) cc_final: 0.7572 (m-80) outliers start: 43 outliers final: 21 residues processed: 231 average time/residue: 1.1915 time to fit residues: 306.5413 Evaluate side-chains 218 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15452 Z= 0.332 Angle : 0.627 14.791 20896 Z= 0.316 Chirality : 0.045 0.206 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.564 18.649 2056 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 2.63 % Allowed : 19.49 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1852 helix: 0.34 (0.19), residues: 736 sheet: -1.04 (0.22), residues: 452 loop : -0.08 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 53 HIS 0.006 0.001 HIS D 32 PHE 0.030 0.002 PHE C 56 TYR 0.019 0.002 TYR A 308 ARG 0.009 0.000 ARG D 459 *********************** 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 246 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7485 (ttp-110) REVERT: A 93 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: A 159 MET cc_start: 0.7675 (tpp) cc_final: 0.7321 (tpp) REVERT: A 258 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7693 (t70) REVERT: B 88 PHE cc_start: 0.8122 (m-80) cc_final: 0.7456 (m-80) REVERT: B 258 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 389 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 395 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: B 411 MET cc_start: 0.4898 (OUTLIER) cc_final: 0.3484 (mpt) REVERT: B 446 CYS cc_start: 0.7707 (m) cc_final: 0.7366 (m) REVERT: B 497 LYS cc_start: 0.8265 (tptt) cc_final: 0.7898 (tttp) REVERT: C 89 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8456 (mptt) REVERT: C 120 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7535 (ptp90) REVERT: C 130 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 166 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7092 (mtp85) REVERT: C 317 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: C 466 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8143 (m) REVERT: C 475 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 37 MET cc_start: 0.8587 (mmm) cc_final: 0.7967 (mmt) REVERT: D 66 PHE cc_start: 0.8047 (m-80) cc_final: 0.7545 (m-80) REVERT: D 99 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7645 (mm-30) outliers start: 43 outliers final: 23 residues processed: 234 average time/residue: 1.2075 time to fit residues: 314.8902 Evaluate side-chains 225 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15452 Z= 0.232 Angle : 0.588 15.930 20896 Z= 0.297 Chirality : 0.044 0.213 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.441 18.774 2056 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 19.73 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1852 helix: 0.49 (0.20), residues: 732 sheet: -0.99 (0.22), residues: 452 loop : -0.10 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 53 HIS 0.005 0.001 HIS D 451 PHE 0.034 0.001 PHE C 56 TYR 0.018 0.001 TYR C 147 ARG 0.009 0.000 ARG D 459 *********************** 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 242 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7446 (ttp-110) REVERT: A 93 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: A 175 ARG cc_start: 0.7880 (ptm160) cc_final: 0.7640 (ptm160) REVERT: A 176 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: A 258 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: B 88 PHE cc_start: 0.8071 (m-80) cc_final: 0.7405 (m-80) REVERT: B 258 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 395 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: B 446 CYS cc_start: 0.7610 (m) cc_final: 0.7314 (m) REVERT: B 497 LYS cc_start: 0.8223 (tptt) cc_final: 0.7856 (tttp) REVERT: C 89 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8445 (mptt) REVERT: C 120 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7561 (ptp90) REVERT: C 130 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 166 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7179 (mtp85) REVERT: C 317 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: C 466 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8135 (m) REVERT: C 475 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 37 MET cc_start: 0.8588 (mmm) cc_final: 0.7948 (mmt) REVERT: D 66 PHE cc_start: 0.8000 (m-80) cc_final: 0.7511 (m-80) REVERT: D 99 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7549 (mm-30) outliers start: 37 outliers final: 20 residues processed: 233 average time/residue: 1.2335 time to fit residues: 318.7314 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15452 Z= 0.273 Angle : 0.608 14.906 20896 Z= 0.306 Chirality : 0.044 0.219 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.480 20.284 2056 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.14 % Allowed : 20.40 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1852 helix: 0.46 (0.20), residues: 732 sheet: -1.00 (0.22), residues: 452 loop : -0.12 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.036 0.002 PHE C 56 TYR 0.020 0.002 TYR A 308 ARG 0.009 0.000 ARG A 498 ********************** 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 229 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7482 (ttp-110) REVERT: A 93 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8000 (pt0) REVERT: A 125 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8522 (mmm) REVERT: A 176 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: A 258 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: B 88 PHE cc_start: 0.8068 (m-80) cc_final: 0.7404 (m-80) REVERT: B 258 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: B 395 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: B 446 CYS cc_start: 0.7613 (m) cc_final: 0.7312 (m) REVERT: B 497 LYS cc_start: 0.8235 (tptt) cc_final: 0.7872 (tttp) REVERT: C 89 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8446 (mptt) REVERT: C 120 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7544 (ptp90) REVERT: C 130 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8165 (tt) REVERT: C 166 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7120 (mtp85) REVERT: C 317 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6234 (tt0) REVERT: C 466 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (m) REVERT: C 475 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 37 MET cc_start: 0.8574 (mmm) cc_final: 0.7941 (mmt) REVERT: D 66 PHE cc_start: 0.7995 (m-80) cc_final: 0.7508 (m-80) REVERT: D 99 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7569 (mm-30) outliers start: 35 outliers final: 22 residues processed: 221 average time/residue: 1.2519 time to fit residues: 306.3119 Evaluate side-chains 219 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120366 restraints weight = 17900.571| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.21 r_work: 0.3286 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 15452 Z= 0.298 Angle : 0.824 59.130 20896 Z= 0.456 Chirality : 0.044 0.197 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.486 20.081 2056 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 20.47 % Favored : 77.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1852 helix: 0.46 (0.20), residues: 732 sheet: -1.01 (0.22), residues: 452 loop : -0.13 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.030 0.001 PHE C 56 TYR 0.018 0.001 TYR A 308 ARG 0.010 0.000 ARG A 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5355.10 seconds wall clock time: 97 minutes 28.35 seconds (5848.35 seconds total)